From d4018658259a382d3f22ced3b43c560e476712b5 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Tue, 4 Jun 2024 16:41:30 +0200
Subject: [PATCH 01/14] wip ship st test

---
 tests/conftest.py                             | 23 ++++++++
 tests/instruments/test_ship_underwater_st.py  | 54 ++++++++++++++++---
 .../instruments/ship_underwater_st.py         | 10 ++--
 virtual_ship/spacetime.py                     |  3 +-
 4 files changed, 80 insertions(+), 10 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index f656c38f..57475f96 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,9 @@
 """Test configuration that is ran for every test."""
 
 import pytest
+import tempfile
+import shutil
+from typing import Generator, Callable
 
 
 @pytest.fixture(autouse=True)
@@ -12,3 +15,23 @@ def change_test_dir(request, monkeypatch):
     :param monkeypatch: -
     """
     monkeypatch.chdir(request.fspath.dirname)
+
+
+@pytest.fixture
+def tmp_dir_factory() -> Generator[Callable[[str], str], None, None]:
+    """
+    Returns a functions that can generate a random directory and returns its path.
+
+    Created directories are automatically deleted after the rest.
+    """
+    created_dirs = []
+
+    def _create_temp_dir(suffix: str):
+        dir_path = tempfile.mkdtemp(suffix=suffix)
+        created_dirs.append(dir_path)
+        return dir_path
+
+    yield _create_temp_dir
+
+    for dir_path in created_dirs:
+        shutil.rmtree(dir_path)
diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index 05de1d49..ac2756c7 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -5,25 +5,67 @@
 
 from virtual_ship import Location, Spacetime
 from virtual_ship.instruments.ship_underwater_st import simulate_ship_underwater_st
+import xarray as xr
+from typing import Callable
 
 
-def test_simulate_ship_underwater_st() -> None:
+def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> None:
     DEPTH = -2
 
+    base_time = np.datetime64("1950-01-01")
+
+    variables = ["salinity", "temperature", "lat", "lon"]
+
+    sample_points = [
+        Spacetime(Location(3, 0), base_time + np.timedelta64(0, "s")),
+        Spacetime(Location(7, 0), base_time + np.timedelta64(1, "s")),
+    ]
+    expected_obs = [
+        {"salinity": 1, "temperature": 2, "lat": 3, "lon": 0},
+        {"salinity": 5, "temperature": 6, "lat": 7, "lon": 0},
+    ]
+
     fieldset = FieldSet.from_data(
-        {"U": 0, "V": 0, "S": 0, "T": 0},
+        {
+            "U": np.zeros((2, 2)),
+            "V": np.zeros((2, 2)),
+            "salinity": [
+                [expected_obs[0]["salinity"], 0],
+                [0, expected_obs[1]["salinity"]],
+            ],
+            "temperature": [
+                [expected_obs[0]["temperature"], 0],
+                [0, expected_obs[1]["temperature"]],
+            ],
+        },
         {
             "lon": 0,
-            "lat": 0,
-            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+            "lat": np.array([expected_obs[0]["lat"], expected_obs[1]["lat"]]),
+            "time": np.array([base_time, base_time + np.timedelta64(1, "s")]),
         },
     )
 
-    sample_points = [Spacetime(Location(0, 0), 0)]
+    out_file_name = tmp_dir_factory(suffix=".zarr")
 
     simulate_ship_underwater_st(
         fieldset=fieldset,
-        out_file_name="test",
+        out_file_name=out_file_name,
         depth=DEPTH,
         sample_points=sample_points,
     )
+
+    results = xr.open_zarr(out_file_name)
+
+    assert len(results.trajectory) == 1
+    assert len(results.sel(trajectory=0).obs == len(sample_points))
+
+    for i, (obs_i, exp) in enumerate(
+        zip(results.sel(trajectory=0).obs, expected_obs, strict=True)
+    ):
+        obs = results.sel(trajectory=0, obs=obs_i)
+        for var in variables:
+            obs_value = obs[var].values.item()
+            exp_value = exp[var]
+            assert np.isclose(
+                obs_value, exp_value
+            ), f"Observation incorrect {i=} {var=} {obs_value=} {exp_value=}."
diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index 389a1e8e..5a5b1e0b 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -15,12 +15,16 @@
 
 # define function sampling Salinity
 def _sample_salinity(particle, fieldset, time):
-    particle.salinity = fieldset.S[time, particle.depth, particle.lat, particle.lon]
+    particle.salinity = fieldset.salinity[
+        time, particle.depth, particle.lat, particle.lon
+    ]
 
 
 # define function sampling Temperature
 def _sample_temperature(particle, fieldset, time):
-    particle.temperature = fieldset.T[time, particle.depth, particle.lat, particle.lon]
+    particle.temperature = fieldset.temperature[
+        time, particle.depth, particle.lat, particle.lon
+    ]
 
 
 def simulate_ship_underwater_st(
@@ -56,7 +60,7 @@ def simulate_ship_underwater_st(
     for point in sample_points:
         particleset.lon_nextloop[:] = point.location.lon
         particleset.lat_nextloop[:] = point.location.lat
-        particleset.time_nextloop[:] = point.time
+        particleset.time_nextloop[:] = fieldset.time_origin.reltime(point.time)
 
         particleset.execute(
             [_sample_salinity, _sample_temperature],
diff --git a/virtual_ship/spacetime.py b/virtual_ship/spacetime.py
index c277e642..c133a4f6 100644
--- a/virtual_ship/spacetime.py
+++ b/virtual_ship/spacetime.py
@@ -3,6 +3,7 @@
 from dataclasses import dataclass
 
 from .location import Location
+import numpy as np
 
 
 @dataclass
@@ -11,4 +12,4 @@ class Spacetime:
     """A location and time."""
 
     location: Location
-    time: float
+    time: np.datetime64

From 6c34b5ea591f279c0387e4fd1fca27bff3405f33 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 16:59:29 +0200
Subject: [PATCH 02/14] finish test

---
 tests/instruments/test_ship_underwater_st.py  | 15 +++++++++----
 .../instruments/ship_underwater_st.py         | 22 +++++++++++++------
 2 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index ac2756c7..738b8f0b 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -7,6 +7,7 @@
 from virtual_ship.instruments.ship_underwater_st import simulate_ship_underwater_st
 import xarray as xr
 from typing import Callable
+from datetime import timedelta
 
 
 def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> None:
@@ -21,8 +22,14 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
         Spacetime(Location(7, 0), base_time + np.timedelta64(1, "s")),
     ]
     expected_obs = [
-        {"salinity": 1, "temperature": 2, "lat": 3, "lon": 0},
-        {"salinity": 5, "temperature": 6, "lat": 7, "lon": 0},
+        {"salinity": 1, "temperature": 2, "lat": 3, "lon": 0, "time": base_time},
+        {
+            "salinity": 5,
+            "temperature": 6,
+            "lat": 7,
+            "lon": 0,
+            "time": base_time + np.timedelta64(1, "s"),
+        },
     ]
 
     fieldset = FieldSet.from_data(
@@ -41,7 +48,7 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
         {
             "lon": 0,
             "lat": np.array([expected_obs[0]["lat"], expected_obs[1]["lat"]]),
-            "time": np.array([base_time, base_time + np.timedelta64(1, "s")]),
+            "time": np.array([expected_obs[0]["time"], expected_obs[1]["time"]]),
         },
     )
 
@@ -57,7 +64,7 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
     results = xr.open_zarr(out_file_name)
 
     assert len(results.trajectory) == 1
-    assert len(results.sel(trajectory=0).obs == len(sample_points))
+    assert len(results.sel(trajectory=0).obs) == len(sample_points)
 
     for i, (obs_i, exp) in enumerate(
         zip(results.sel(trajectory=0).obs, expected_obs, strict=True)
diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index 5a5b1e0b..fcd36c13 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -1,11 +1,14 @@
 """Ship salinity and temperature."""
 
 import numpy as np
-from parcels import FieldSet, JITParticle, ParticleSet, Variable
+from parcels import FieldSet, ScipyParticle, ParticleSet, Variable
 
 from ..spacetime import Spacetime
 
-_ShipSTParticle = JITParticle.add_variables(
+# we specifically use ScipyParticle because we have many small calls to execute
+# JITParticle would require compilation every time
+# this ends up being faster
+_ShipSTParticle = ScipyParticle.add_variables(
     [
         Variable("salinity", dtype=np.float32, initial=np.nan),
         Variable("temperature", dtype=np.float32, initial=np.nan),
@@ -40,32 +43,37 @@ def simulate_ship_underwater_st(
     :param out_file_name: The file to write the results to.
     :param depth: The depth at which to measure. 0 is water surface, negative is into the water.
     :param sample_points: The places and times to sample at.
+    :param sample_dt: Time between each sample point.
+    :param output_dt: Period of writing to output file.
     """
     sample_points.sort(key=lambda p: p.time)
 
     particleset = ParticleSet.from_list(
         fieldset=fieldset,
         pclass=_ShipSTParticle,
-        lon=0.0,  # initial lat/lon are irrelevant and will be overruled later.
+        lon=0.0,  # initial lat/lon are irrelevant and will be overruled later
         lat=0.0,
         depth=depth,
         time=0,  # same for time
     )
 
     # define output file for the simulation
-    out_file = particleset.ParticleFile(
-        name=out_file_name,
-    )
+    # the default outputdt is good(infinite), as we want to just want to write at the end of every call to 'execute'
+    out_file = particleset.ParticleFile(name=out_file_name)
 
+    # iterate over each points, manually set lat lon time, then
+    # execute the particle set for one step, performing one set of measurement
     for point in sample_points:
         particleset.lon_nextloop[:] = point.location.lon
         particleset.lat_nextloop[:] = point.location.lat
         particleset.time_nextloop[:] = fieldset.time_origin.reltime(point.time)
 
+        # perform one step using the particleset
+        # dt and runtime are set so exactly one step is made.
         particleset.execute(
             [_sample_salinity, _sample_temperature],
             dt=1,
             runtime=1,
             verbose_progress=False,
+            output_file=out_file,
         )
-        out_file.write(particleset, time=particleset[0].time)

From 8184c745401ad6385d435c02cc29de5a429694a2 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:07:27 +0200
Subject: [PATCH 03/14] explicitly use the trajectory listed in zarr

---
 tests/instruments/test_ship_underwater_st.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index 738b8f0b..71cba266 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -64,12 +64,13 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
     results = xr.open_zarr(out_file_name)
 
     assert len(results.trajectory) == 1
-    assert len(results.sel(trajectory=0).obs) == len(sample_points)
+    traj = results.trajectory.item()
+    assert len(results.sel(trajectory=traj).obs) == len(sample_points)
 
     for i, (obs_i, exp) in enumerate(
-        zip(results.sel(trajectory=0).obs, expected_obs, strict=True)
+        zip(results.sel(trajectory=traj).obs, expected_obs, strict=True)
     ):
-        obs = results.sel(trajectory=0, obs=obs_i)
+        obs = results.sel(trajectory=traj, obs=obs_i)
         for var in variables:
             obs_value = obs[var].values.item()
             exp_value = exp[var]

From 68db417c5f951eb5fc0434293e19cc480033d969 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:20:55 +0200
Subject: [PATCH 04/14] improve comments in test

---
 tests/instruments/test_ship_underwater_st.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index 71cba266..15b0adf6 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -7,20 +7,25 @@
 from virtual_ship.instruments.ship_underwater_st import simulate_ship_underwater_st
 import xarray as xr
 from typing import Callable
-from datetime import timedelta
 
 
 def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> None:
+    # depth at which the sampling will be done
     DEPTH = -2
 
+    # arbitrary time offset for the dummy fieldset
     base_time = np.datetime64("1950-01-01")
 
+    # variabes we are going to compare between expected and actual observations
     variables = ["salinity", "temperature", "lat", "lon"]
 
+    # were to sample
     sample_points = [
         Spacetime(Location(3, 0), base_time + np.timedelta64(0, "s")),
         Spacetime(Location(7, 0), base_time + np.timedelta64(1, "s")),
     ]
+
+    # expected observations at sample points
     expected_obs = [
         {"salinity": 1, "temperature": 2, "lat": 3, "lon": 0, "time": base_time},
         {
@@ -32,6 +37,7 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
         },
     ]
 
+    # create fieldset based on the expected observations
     fieldset = FieldSet.from_data(
         {
             "U": np.zeros((2, 2)),
@@ -63,10 +69,14 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
 
     results = xr.open_zarr(out_file_name)
 
-    assert len(results.trajectory) == 1
+    # below we assert if output makes sense
+    assert len(results.trajectory) == 1  # expect a singe trajectory
     traj = results.trajectory.item()
-    assert len(results.sel(trajectory=traj).obs) == len(sample_points)
+    assert len(results.sel(trajectory=traj).obs) == len(
+        sample_points
+    )  # expect as many obs as sample points
 
+    # for every obs, check if the variables match the expected observations
     for i, (obs_i, exp) in enumerate(
         zip(results.sel(trajectory=traj).obs, expected_obs, strict=True)
     ):

From a790c25ac7e49ffc74140184c18c7aa3445b54b4 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:22:59 +0200
Subject: [PATCH 05/14] docstring improvements

---
 tests/conftest.py                              | 11 +++++++----
 tests/instruments/test_ship_underwater_st.py   |  5 +++--
 virtual_ship/instruments/ship_underwater_st.py |  4 +---
 virtual_ship/spacetime.py                      |  3 ++-
 4 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 57475f96..da9a4e83 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,9 +1,10 @@
 """Test configuration that is ran for every test."""
 
-import pytest
-import tempfile
 import shutil
-from typing import Generator, Callable
+import tempfile
+from typing import Callable, Generator
+
+import pytest
 
 
 @pytest.fixture(autouse=True)
@@ -20,9 +21,11 @@ def change_test_dir(request, monkeypatch):
 @pytest.fixture
 def tmp_dir_factory() -> Generator[Callable[[str], str], None, None]:
     """
-    Returns a functions that can generate a random directory and returns its path.
+    Return a function that can generate a random directory and returns its path.
 
     Created directories are automatically deleted after the rest.
+
+    :yields: A generator for temporary directories that will be automatically removed.
     """
     created_dirs = []
 
diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index 15b0adf6..e7564280 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -1,12 +1,13 @@
 """Test the simulation of ship salinity temperature measurements."""
 
+from typing import Callable
+
 import numpy as np
+import xarray as xr
 from parcels import FieldSet
 
 from virtual_ship import Location, Spacetime
 from virtual_ship.instruments.ship_underwater_st import simulate_ship_underwater_st
-import xarray as xr
-from typing import Callable
 
 
 def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> None:
diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index fcd36c13..affb2a11 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -1,7 +1,7 @@
 """Ship salinity and temperature."""
 
 import numpy as np
-from parcels import FieldSet, ScipyParticle, ParticleSet, Variable
+from parcels import FieldSet, ParticleSet, ScipyParticle, Variable
 
 from ..spacetime import Spacetime
 
@@ -43,8 +43,6 @@ def simulate_ship_underwater_st(
     :param out_file_name: The file to write the results to.
     :param depth: The depth at which to measure. 0 is water surface, negative is into the water.
     :param sample_points: The places and times to sample at.
-    :param sample_dt: Time between each sample point.
-    :param output_dt: Period of writing to output file.
     """
     sample_points.sort(key=lambda p: p.time)
 
diff --git a/virtual_ship/spacetime.py b/virtual_ship/spacetime.py
index c133a4f6..68985669 100644
--- a/virtual_ship/spacetime.py
+++ b/virtual_ship/spacetime.py
@@ -2,9 +2,10 @@
 
 from dataclasses import dataclass
 
-from .location import Location
 import numpy as np
 
+from .location import Location
+
 
 @dataclass
 # TODO I take suggestions for a better name

From 8ee267b300e976815d6360d1c60d27b3a6de8411 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:24:24 +0200
Subject: [PATCH 06/14] fix typo

---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index da9a4e83..5a0f5a65 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -23,7 +23,7 @@ def tmp_dir_factory() -> Generator[Callable[[str], str], None, None]:
     """
     Return a function that can generate a random directory and returns its path.
 
-    Created directories are automatically deleted after the rest.
+    Created directories are automatically deleted after the test.
 
     :yields: A generator for temporary directories that will be automatically removed.
     """

From 4c04e47919aeb85e5098a7d44a5656c2081372a8 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:25:24 +0200
Subject: [PATCH 07/14] fix typo

---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 5a0f5a65..f749d1da 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -21,7 +21,7 @@ def change_test_dir(request, monkeypatch):
 @pytest.fixture
 def tmp_dir_factory() -> Generator[Callable[[str], str], None, None]:
     """
-    Return a function that can generate a random directory and returns its path.
+    Yields a function that can generate a random directory and returns its path.
 
     Created directories are automatically deleted after the test.
 

From 250344c0ffb8fbb2fae78ef62f3560658321a8ee Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:26:32 +0200
Subject: [PATCH 08/14] fix typo

---
 tests/instruments/test_ship_underwater_st.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index e7564280..8ba55561 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -20,7 +20,7 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
     # variabes we are going to compare between expected and actual observations
     variables = ["salinity", "temperature", "lat", "lon"]
 
-    # were to sample
+    # where to sample
     sample_points = [
         Spacetime(Location(3, 0), base_time + np.timedelta64(0, "s")),
         Spacetime(Location(7, 0), base_time + np.timedelta64(1, "s")),

From 6a936cbef2352c2084733f4b7c64a34753bb80f6 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Wed, 5 Jun 2024 17:40:19 +0200
Subject: [PATCH 09/14] spacetime time now datetime object isntead of numpy

---
 tests/conftest.py                             |  2 +-
 tests/instruments/test_ship_underwater_st.py  | 24 ++++++++++++++-----
 .../instruments/ship_underwater_st.py         |  4 +++-
 virtual_ship/spacetime.py                     |  5 ++--
 4 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index f749d1da..dfeb93b7 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -21,7 +21,7 @@ def change_test_dir(request, monkeypatch):
 @pytest.fixture
 def tmp_dir_factory() -> Generator[Callable[[str], str], None, None]:
     """
-    Yields a function that can generate a random directory and returns its path.
+    Yield functions that can generate a random directory and returns its path.
 
     Created directories are automatically deleted after the test.
 
diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index 8ba55561..b1294557 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -1,5 +1,6 @@
 """Test the simulation of ship salinity temperature measurements."""
 
+import datetime
 from typing import Callable
 
 import numpy as np
@@ -15,26 +16,32 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
     DEPTH = -2
 
     # arbitrary time offset for the dummy fieldset
-    base_time = np.datetime64("1950-01-01")
+    base_time = datetime.datetime.strptime("1950-01-01", "%Y-%m-%d")
 
     # variabes we are going to compare between expected and actual observations
     variables = ["salinity", "temperature", "lat", "lon"]
 
     # where to sample
     sample_points = [
-        Spacetime(Location(3, 0), base_time + np.timedelta64(0, "s")),
-        Spacetime(Location(7, 0), base_time + np.timedelta64(1, "s")),
+        Spacetime(Location(3, 0), base_time + datetime.timedelta(seconds=0)),
+        Spacetime(Location(7, 0), base_time + datetime.timedelta(seconds=1)),
     ]
 
     # expected observations at sample points
     expected_obs = [
-        {"salinity": 1, "temperature": 2, "lat": 3, "lon": 0, "time": base_time},
+        {
+            "salinity": 1,
+            "temperature": 2,
+            "lat": 3,
+            "lon": 0,
+            "time": base_time + datetime.timedelta(seconds=0),
+        },
         {
             "salinity": 5,
             "temperature": 6,
             "lat": 7,
             "lon": 0,
-            "time": base_time + np.timedelta64(1, "s"),
+            "time": base_time + datetime.timedelta(seconds=1),
         },
     ]
 
@@ -55,7 +62,12 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
         {
             "lon": 0,
             "lat": np.array([expected_obs[0]["lat"], expected_obs[1]["lat"]]),
-            "time": np.array([expected_obs[0]["time"], expected_obs[1]["time"]]),
+            "time": np.array(
+                [
+                    np.datetime64(expected_obs[0]["time"]),
+                    np.datetime64(expected_obs[1]["time"]),
+                ]
+            ),
         },
     )
 
diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index affb2a11..323baec0 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -64,7 +64,9 @@ def simulate_ship_underwater_st(
     for point in sample_points:
         particleset.lon_nextloop[:] = point.location.lon
         particleset.lat_nextloop[:] = point.location.lat
-        particleset.time_nextloop[:] = fieldset.time_origin.reltime(point.time)
+        particleset.time_nextloop[:] = fieldset.time_origin.reltime(
+            np.datetime64(point.time)
+        )
 
         # perform one step using the particleset
         # dt and runtime are set so exactly one step is made.
diff --git a/virtual_ship/spacetime.py b/virtual_ship/spacetime.py
index 68985669..03804975 100644
--- a/virtual_ship/spacetime.py
+++ b/virtual_ship/spacetime.py
@@ -1,8 +1,7 @@
 """Location class. See class description."""
 
 from dataclasses import dataclass
-
-import numpy as np
+from datetime import datetime
 
 from .location import Location
 
@@ -13,4 +12,4 @@ class Spacetime:
     """A location and time."""
 
     location: Location
-    time: np.datetime64
+    time: datetime

From d09b368b724fc842e12b9769874d47c22ab8c35b Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Thu, 6 Jun 2024 12:41:22 +0200
Subject: [PATCH 10/14] use builtin tmpdir pytest

---
 tests/conftest.py                             | 28 +------------------
 tests/instruments/test_ship_underwater_st.py  | 10 +++----
 .../instruments/ship_underwater_st.py         |  7 +++--
 3 files changed, 10 insertions(+), 35 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index dfeb93b7..1159768d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,14 +1,10 @@
 """Test configuration that is ran for every test."""
 
-import shutil
-import tempfile
-from typing import Callable, Generator
-
 import pytest
 
 
 @pytest.fixture(autouse=True)
-def change_test_dir(request, monkeypatch):
+def test_in_working_dir(request, monkeypatch):
     """
     Set the working directory for each test to the directory of that test.
 
@@ -16,25 +12,3 @@ def change_test_dir(request, monkeypatch):
     :param monkeypatch: -
     """
     monkeypatch.chdir(request.fspath.dirname)
-
-
-@pytest.fixture
-def tmp_dir_factory() -> Generator[Callable[[str], str], None, None]:
-    """
-    Yield functions that can generate a random directory and returns its path.
-
-    Created directories are automatically deleted after the test.
-
-    :yields: A generator for temporary directories that will be automatically removed.
-    """
-    created_dirs = []
-
-    def _create_temp_dir(suffix: str):
-        dir_path = tempfile.mkdtemp(suffix=suffix)
-        created_dirs.append(dir_path)
-        return dir_path
-
-    yield _create_temp_dir
-
-    for dir_path in created_dirs:
-        shutil.rmtree(dir_path)
diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index b1294557..582129b4 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -1,9 +1,9 @@
 """Test the simulation of ship salinity temperature measurements."""
 
 import datetime
-from typing import Callable
 
 import numpy as np
+import py
 import xarray as xr
 from parcels import FieldSet
 
@@ -11,7 +11,7 @@
 from virtual_ship.instruments.ship_underwater_st import simulate_ship_underwater_st
 
 
-def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> None:
+def test_simulate_ship_underwater_st(tmpdir: py.path.LocalPath) -> None:
     # depth at which the sampling will be done
     DEPTH = -2
 
@@ -71,16 +71,16 @@ def test_simulate_ship_underwater_st(tmp_dir_factory: Callable[[str], str]) -> N
         },
     )
 
-    out_file_name = tmp_dir_factory(suffix=".zarr")
+    out_path = tmpdir.join("out.zarr")
 
     simulate_ship_underwater_st(
         fieldset=fieldset,
-        out_file_name=out_file_name,
+        out_path=out_path,
         depth=DEPTH,
         sample_points=sample_points,
     )
 
-    results = xr.open_zarr(out_file_name)
+    results = xr.open_zarr(out_path)
 
     # below we assert if output makes sense
     assert len(results.trajectory) == 1  # expect a singe trajectory
diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index 323baec0..9d4940d9 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -1,6 +1,7 @@
 """Ship salinity and temperature."""
 
 import numpy as np
+import py
 from parcels import FieldSet, ParticleSet, ScipyParticle, Variable
 
 from ..spacetime import Spacetime
@@ -32,7 +33,7 @@ def _sample_temperature(particle, fieldset, time):
 
 def simulate_ship_underwater_st(
     fieldset: FieldSet,
-    out_file_name: str,
+    out_path: str | py.path.LocalPath,
     depth: float,
     sample_points: list[Spacetime],
 ) -> None:
@@ -40,7 +41,7 @@ def simulate_ship_underwater_st(
     Use parcels to simulate underway data, measuring salinity and temperature at the given depth along the ship track in a fieldset.
 
     :param fieldset: The fieldset to simulate the sampling in.
-    :param out_file_name: The file to write the results to.
+    :param out_path: The path to write the results to.
     :param depth: The depth at which to measure. 0 is water surface, negative is into the water.
     :param sample_points: The places and times to sample at.
     """
@@ -57,7 +58,7 @@ def simulate_ship_underwater_st(
 
     # define output file for the simulation
     # the default outputdt is good(infinite), as we want to just want to write at the end of every call to 'execute'
-    out_file = particleset.ParticleFile(name=out_file_name)
+    out_file = particleset.ParticleFile(name=out_path)
 
     # iterate over each points, manually set lat lon time, then
     # execute the particle set for one step, performing one set of measurement

From ac87bf8c99fb4b4460cc5f23d35595f6b7b859e9 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Mon, 10 Jun 2024 13:58:10 +0200
Subject: [PATCH 11/14] remove unused iteration variable

---
 tests/instruments/test_ship_underwater_st.py | 6 ++----
 virtual_ship/sailship.py                     | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
index 582129b4..784ff4cc 100644
--- a/tests/instruments/test_ship_underwater_st.py
+++ b/tests/instruments/test_ship_underwater_st.py
@@ -90,13 +90,11 @@ def test_simulate_ship_underwater_st(tmpdir: py.path.LocalPath) -> None:
     )  # expect as many obs as sample points
 
     # for every obs, check if the variables match the expected observations
-    for i, (obs_i, exp) in enumerate(
-        zip(results.sel(trajectory=traj).obs, expected_obs, strict=True)
-    ):
+    for obs_i, exp in zip(results.sel(trajectory=traj).obs, expected_obs, strict=True):
         obs = results.sel(trajectory=traj, obs=obs_i)
         for var in variables:
             obs_value = obs[var].values.item()
             exp_value = exp[var]
             assert np.isclose(
                 obs_value, exp_value
-            ), f"Observation incorrect {i=} {var=} {obs_value=} {exp_value=}."
+            ), f"Observation incorrect {obs_i=} {var=} {obs_value=} {exp_value=}."
diff --git a/virtual_ship/sailship.py b/virtual_ship/sailship.py
index 62bf5767..928756c6 100644
--- a/virtual_ship/sailship.py
+++ b/virtual_ship/sailship.py
@@ -195,7 +195,7 @@ def sailship(config: VirtualShipConfiguration):
     print("Simulating onboard salinity and temperature measurements.")
     simulate_ship_underwater_st(
         fieldset=config.ship_underwater_st_fieldset,
-        out_file_name=os.path.join("results", "ship_underwater_st.zarr"),
+        out_path=os.path.join("results", "ship_underwater_st.zarr"),
         depth=-2,
         sample_points=ship_underwater_sts,
     )

From dfd52ea086865aa659a5f964163dff492e8293b2 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Mon, 10 Jun 2024 14:01:34 +0200
Subject: [PATCH 12/14] explicitly use outputdt inf

---
 virtual_ship/instruments/ship_underwater_st.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index 9d4940d9..eeb2fd25 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -57,8 +57,8 @@ def simulate_ship_underwater_st(
     )
 
     # define output file for the simulation
-    # the default outputdt is good(infinite), as we want to just want to write at the end of every call to 'execute'
-    out_file = particleset.ParticleFile(name=out_path)
+    # outputdt set to infinie as we want to just want to write at the end of every call to 'execute'
+    out_file = particleset.ParticleFile(name=out_path, outputdt=np.inf)
 
     # iterate over each points, manually set lat lon time, then
     # execute the particle set for one step, performing one set of measurement

From 8b9855b27ba4fe3688929bb7a977096a3a43c443 Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Mon, 10 Jun 2024 14:01:53 +0200
Subject: [PATCH 13/14] typo

---
 virtual_ship/instruments/ship_underwater_st.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index eeb2fd25..99416c0c 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -60,7 +60,7 @@ def simulate_ship_underwater_st(
     # outputdt set to infinie as we want to just want to write at the end of every call to 'execute'
     out_file = particleset.ParticleFile(name=out_path, outputdt=np.inf)
 
-    # iterate over each points, manually set lat lon time, then
+    # iterate over each point, manually set lat lon time, then
     # execute the particle set for one step, performing one set of measurement
     for point in sample_points:
         particleset.lon_nextloop[:] = point.location.lon

From 1c5c3d2a860e07a69c72abdc096a1cb15a22146b Mon Sep 17 00:00:00 2001
From: Aart Stuurman <aartstuurman@hotmail.com>
Date: Mon, 10 Jun 2024 18:13:26 +0200
Subject: [PATCH 14/14] comment

---
 virtual_ship/instruments/ship_underwater_st.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/virtual_ship/instruments/ship_underwater_st.py b/virtual_ship/instruments/ship_underwater_st.py
index 99416c0c..b2226381 100644
--- a/virtual_ship/instruments/ship_underwater_st.py
+++ b/virtual_ship/instruments/ship_underwater_st.py
@@ -7,8 +7,7 @@
 from ..spacetime import Spacetime
 
 # we specifically use ScipyParticle because we have many small calls to execute
-# JITParticle would require compilation every time
-# this ends up being faster
+# there is some overhead with JITParticle and this ends up being significantly faster
 _ShipSTParticle = ScipyParticle.add_variables(
     [
         Variable("salinity", dtype=np.float32, initial=np.nan),