Merge branch 'master' into harmonise_field_interp_order

Author: erikvansebille

.github/release.yaml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/ci.yml

@@ -45,7 +45,7 @@ jobs:
           coverage run -m pytest -v -s --html=${{ matrix.os }}_${{ matrix.python-version }}_unit_test_report.html --self-contained-html tests
           coverage xml
       - name: Codecov
-        uses: codecov/codecov-action@v5.0.7
+        uses: codecov/codecov-action@v5.1.2
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         if: matrix.python-version == '3.13'
@@ -80,7 +80,7 @@ jobs:
           coverage run -m pytest -v -s --nbval-lax -k "not documentation" --html="${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html" --self-contained-html docs/examples
           coverage xml
       - name: Codecov
-        uses: codecov/codecov-action@v5.0.7
+        uses: codecov/codecov-action@v5.1.2
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
@@ -117,7 +117,7 @@ jobs:
         run: |
           mypy --install-types --non-interactive parcels --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v5.0.7
+        uses: codecov/codecov-action@v5.1.2
         if: ${{ always() }} # Upload even on error of mypy
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pypi-release.yml

@@ -72,7 +72,7 @@ jobs:
 
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/[email protected].2
+        uses: pypa/[email protected].3
         with:
           user: __token__
           password: ${{ secrets.PARCELS_PYPI_TEST_TOKEN }}
@@ -89,7 +89,7 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/[email protected].2
+        uses: pypa/[email protected].3
         with:
           user: __token__
           password: ${{ secrets.PARCELS_PYPI_PROD_TOKEN }}

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
         types: [text]
         files: \.(json|ipynb)$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.3
+    rev: v0.8.6
     hooks:
       - id: ruff
         name: ruff lint (.py)

docs/examples/tutorial_periodic_boundaries.ipynb

@@ -42,7 +42,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In case of 'simple' models on an A-grid, the idea in Parcels is to do two things:\n",
+    "If you have a 'simple' `Rectilinear` A-grid, you can create periodic boundaries in Parcels in two steps:\n",
     "\n",
     "1. Extend the fieldset with a small 'halo'\n",
     "2. Add a periodic boundary kernel to the `.execute`\n"

parcels/grid.py

@@ -694,53 +694,9 @@ def add_periodic_halo(self, zonal, meridional, halosize=5):
         halosize : int
             size of the halo (in grid points). Default is 5 grid points
         """
-        if zonal:
-            lonshift = self.lon[:, -1] - 2 * self.lon[:, 0] + self.lon[:, 1]
-            if not np.allclose(self.lon[:, 1] - self.lon[:, 0], self.lon[:, -1] - self.lon[:, -2]):
-                warnings.warn(
-                    "The zonal halo is located at the east and west of current grid, "
-                    "with a dx = lon[1]-lon[0] between the last nodes of the original grid and the first ones of the halo. "
-                    "In your grid, lon[1]-lon[0] != lon[-1]-lon[-2]. Is the halo computed as you expect?",
-                    FieldSetWarning,
-                    stacklevel=2,
-                )
-            self._lon = np.concatenate(
-                (
-                    self.lon[:, -halosize:] - lonshift[:, np.newaxis],
-                    self.lon,
-                    self.lon[:, 0:halosize] + lonshift[:, np.newaxis],
-                ),
-                axis=len(self.lon.shape) - 1,
-            )
-            self._lat = np.concatenate(
-                (self.lat[:, -halosize:], self.lat, self.lat[:, 0:halosize]), axis=len(self.lat.shape) - 1
-            )
-            self._zonal_periodic = True
-            self._zonal_halo = halosize
-        if meridional:
-            if not np.allclose(self.lat[1, :] - self.lat[0, :], self.lat[-1, :] - self.lat[-2, :]):
-                warnings.warn(
-                    "The meridional halo is located at the north and south of current grid, "
-                    "with a dy = lat[1]-lat[0] between the last nodes of the original grid and the first ones of the halo. "
-                    "In your grid, lat[1]-lat[0] != lat[-1]-lat[-2]. Is the halo computed as you expect?",
-                    FieldSetWarning,
-                    stacklevel=2,
-                )
-            latshift = self.lat[-1, :] - 2 * self.lat[0, :] + self.lat[1, :]
-            self._lat = np.concatenate(
-                (
-                    self.lat[-halosize:, :] - latshift[np.newaxis, :],
-                    self.lat,
-                    self.lat[0:halosize, :] + latshift[np.newaxis, :],
-                ),
-                axis=len(self.lat.shape) - 2,
-            )
-            self._lon = np.concatenate(
-                (self.lon[-halosize:, :], self.lon, self.lon[0:halosize, :]), axis=len(self.lon.shape) - 2
-            )
-            self._meridional_halo = halosize
-        if isinstance(self, CurvilinearSGrid):
-            self._add_Sdepth_periodic_halo(zonal, meridional, halosize)
+        raise NotImplementedError(
+            "CurvilinearGrid does not support add_periodic_halo. See https://github.com/OceanParcels/Parcels/pull/1811"
+        )
 
 
 class CurvilinearZGrid(CurvilinearGrid):

tests/test_fieldset.py

@@ -565,7 +565,8 @@ def test_curv_fieldset_add_periodic_halo():
     dimensions = {"dx": {"lon": "glamu", "lat": "gphiu"}, "dy": {"lon": "glamu", "lat": "gphiu"}}
     fieldset = FieldSet.from_nemo(filenames, variables, dimensions)
 
-    fieldset.add_periodic_halo(zonal=3, meridional=2)
+    with pytest.raises(NotImplementedError):
+        fieldset.add_periodic_halo(zonal=3, meridional=2)
 
 
 @pytest.mark.parametrize("mesh", ["flat", "spherical"])

tests/test_particlefile.py

@@ -334,6 +334,24 @@ def Update_lon(particle, fieldset, time):
     assert np.allclose(pset.lon, 0.6)
 
 
+@pytest.mark.parametrize("mode", ["scipy", "jit"])
+def test_correct_misaligned_outputdt_dt(fieldset, mode, tmp_zarrfile):
+    """Testing that outputdt does not need to be a multiple of dt."""
+
+    def Update_lon(particle, fieldset, time):
+        particle_dlon += particle.dt  # noqa
+
+    pset = ParticleSet(fieldset, pclass=ptype[mode], lon=[0], lat=[0], lonlatdepth_dtype=np.float64)
+    ofile = pset.ParticleFile(name=tmp_zarrfile, outputdt=3)
+    pset.execute(pset.Kernel(Update_lon), endtime=11, dt=2, output_file=ofile)
+
+    ds = xr.open_zarr(tmp_zarrfile)
+    assert np.allclose(ds.lon.values, [0, 3, 6, 9])
+    assert np.allclose(
+        ds.time.values[0, :], [np.timedelta64(t, "s") for t in [0, 3, 6, 9]], atol=np.timedelta64(1, "ns")
+    )
+
+
 def setup_pset_execute(*, fieldset: FieldSet, outputdt: timedelta, execute_kwargs, particle_class=ScipyParticle):
     npart = 10