Merge branch 'master' into timeconverter_precision

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/application_kernels/advection.py

@@ -184,8 +184,8 @@ def AdvectionAnalytical(particle, fieldset, time):
         time_i = np.linspace(0, fieldset.U.grid.time[ti + 1] - fieldset.U.grid.time[ti], I_s)
         ds_t = min(ds_t, time_i[np.where(time - fieldset.U.grid.time[ti] < time_i)[0][0]])
 
-    xsi, eta, zeta, xi, yi, zi = fieldset.U._search_indices(
-        particle.lon, particle.lat, particle.depth, particle=particle
+    zeta, eta, xsi, zi, yi, xi = fieldset.U._search_indices(
+        -1, particle.depth, particle.lat, particle.lon, particle=particle
     )
     if withW:
         if abs(xsi - 1) < tol:
@@ -232,14 +232,14 @@ def AdvectionAnalytical(particle, fieldset, time):
     else:
         dz = 1.0
 
-    c1 = fieldset.UV.dist(px[0], px[1], py[0], py[1], grid.mesh, np.dot(i_u.phi2D_lin(xsi, 0.0), py))
-    c2 = fieldset.UV.dist(px[1], px[2], py[1], py[2], grid.mesh, np.dot(i_u.phi2D_lin(1.0, eta), py))
-    c3 = fieldset.UV.dist(px[2], px[3], py[2], py[3], grid.mesh, np.dot(i_u.phi2D_lin(xsi, 1.0), py))
-    c4 = fieldset.UV.dist(px[3], px[0], py[3], py[0], grid.mesh, np.dot(i_u.phi2D_lin(0.0, eta), py))
+    c1 = fieldset.UV.dist(py[0], py[1], px[0], px[1], grid.mesh, np.dot(i_u.phi2D_lin(0.0, xsi), py))
+    c2 = fieldset.UV.dist(py[1], py[2], px[1], px[2], grid.mesh, np.dot(i_u.phi2D_lin(eta, 1.0), py))
+    c3 = fieldset.UV.dist(py[2], py[3], px[2], px[3], grid.mesh, np.dot(i_u.phi2D_lin(1.0, xsi), py))
+    c4 = fieldset.UV.dist(py[3], py[0], px[3], px[0], grid.mesh, np.dot(i_u.phi2D_lin(eta, 0.0), py))
     rad = np.pi / 180.0
     deg2m = 1852 * 60.0
     meshJac = (deg2m * deg2m * math.cos(rad * particle.lat)) if grid.mesh == "spherical" else 1
-    dxdy = fieldset.UV.jacobian(xsi, eta, px, py) * meshJac
+    dxdy = fieldset.UV.jacobian(py, px, eta, xsi) * meshJac
 
     if withW:
         U0 = direction * fieldset.U.data[ti, zi + 1, yi + 1, xi] * c4 * dz

parcels/compilation/codegenerator.py

@@ -834,7 +834,7 @@ def visit_FieldEvalNode(self, node):
             statements_croco = [
                 c.Statement(f"float cs_w[] = {*Cs_w, }".replace("(", "{").replace(")", "}")),
                 c.Statement(
-                    f"{node.var} = croco_from_z_to_sigma(U, H, Zeta, {args[3]}, {args[2]}, {args[1]}, time, &particles->xi[pnum*ngrid], &particles->yi[pnum*ngrid], &particles->zi[pnum*ngrid], &particles->ti[pnum*ngrid], hc, &cs_w)"
+                    f"{node.var} = croco_from_z_to_sigma(time, {args[1]}, {args[2]}, {args[3]}, U, H, Zeta, &particles->ti[pnum*ngrid], &particles->zi[pnum*ngrid], &particles->yi[pnum*ngrid], &particles->xi[pnum*ngrid], hc, &cs_w)"
                 ),
             ]
             args = (args[0], node.var, args[2], args[3])
@@ -863,7 +863,7 @@ def visit_VectorFieldEvalNode(self, node):
             statements_croco = [
                 c.Statement(f"float cs_w[] = {*Cs_w, }".replace("(", "{").replace(")", "}")),
                 c.Statement(
-                    f"{node.var4} = croco_from_z_to_sigma(U, H, Zeta, {args[3]}, {args[2]}, {args[1]}, time, &particles->xi[pnum*ngrid], &particles->yi[pnum*ngrid], &particles->zi[pnum*ngrid], &particles->ti[pnum*ngrid], hc, &cs_w)"
+                    f"{node.var4} = croco_from_z_to_sigma(time, {args[1]}, {args[2]}, {args[3]}, U, H, Zeta, &particles->ti[pnum*ngrid], &particles->zi[pnum*ngrid], &particles->yi[pnum*ngrid], &particles->xi[pnum*ngrid], hc, &cs_w)"
                 ),
             ]
             args = (args[0], node.var4, args[2], args[3])