Merge branch 'v4-dev' into implementing_field_interpolation_api

Author: erikvansebille

.github/workflows/cache-pixi-lock.yml

@@ -17,6 +17,7 @@ jobs:
       - uses: actions/checkout@v5
         with:
           fetch-depth: 0
+          submodules: recursive
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m-%d')" >> "$GITHUB_OUTPUT"

docs/documentation/index.md

@@ -42,7 +42,7 @@ The tutorials written for Parcels v3 are currently being updated for Parcels v4.
 :name: tutorial-kernels
 
 <!-- ../examples/tutorial_diffusion.ipynb -->
-<!-- ../examples/tutorial_sampling.ipynb -->
+../examples/tutorial_sampling.ipynb
 <!-- ../examples/tutorial_particle_field_interaction.ipynb -->
 <!-- ../examples/tutorial_interaction.ipynb -->
 <!-- ../examples/tutorial_analyticaladvection.ipynb -->

docs/examples/tutorial_Argofloats.ipynb

@@ -41,11 +41,9 @@
     "\n",
     "    def SinkingPhase(p):\n",
     "        \"\"\"Phase 0: Sinking with vertical_speed until depth is driftdepth\"\"\"\n",
-    "        p.ddepth += vertical_speed * dt\n",
-    "        p.cycle_phase = np.where(p.depth + p.ddepth >= driftdepth, 1, p.cycle_phase)\n",
-    "        p.ddepth = np.where(\n",
-    "            p.depth + p.ddepth >= driftdepth, driftdepth - p.depth, p.ddepth\n",
-    "        )\n",
+    "        p.dz += vertical_speed * dt\n",
+    "        p.cycle_phase = np.where(p.z + p.dz >= driftdepth, 1, p.cycle_phase)\n",
+    "        p.dz = np.where(p.z + p.dz >= driftdepth, driftdepth - p.z, p.dz)\n",
     "\n",
     "    SinkingPhase(particles[particles.cycle_phase == 0])\n",
     "\n",
@@ -67,11 +65,9 @@
     "\n",
     "    def SecondSinkingPhase(p):\n",
     "        \"\"\"Phase 2: Sinking further to maxdepth\"\"\"\n",
-    "        p.ddepth += vertical_speed * dt\n",
-    "        p.cycle_phase = np.where(p.depth + p.ddepth >= maxdepth, 3, p.cycle_phase)\n",
-    "        p.ddepth = np.where(\n",
-    "            p.depth + p.ddepth >= maxdepth, maxdepth - p.depth, p.ddepth\n",
-    "        )\n",
+    "        p.dz += vertical_speed * dt\n",
+    "        p.cycle_phase = np.where(p.z + p.dz >= maxdepth, 3, p.cycle_phase)\n",
+    "        p.dz = np.where(p.z + p.dz >= maxdepth, maxdepth - p.z, p.dz)\n",
     "\n",
     "    SecondSinkingPhase(particles[particles.cycle_phase == 2])\n",
     "\n",
@@ -81,15 +77,13 @@
     "\n",
     "    def RisingPhase(p):\n",
     "        \"\"\"Phase 3: Rising with vertical_speed until at surface\"\"\"\n",
-    "        p.ddepth -= vertical_speed * dt\n",
-    "        p.temp = fieldset.thetao[p.time, p.depth, p.lat, p.lon]\n",
-    "        p.cycle_phase = np.where(\n",
-    "            p.depth + p.ddepth <= fieldset.mindepth, 4, p.cycle_phase\n",
-    "        )\n",
-    "        p.ddepth = np.where(\n",
-    "            p.depth + p.ddepth <= fieldset.mindepth,\n",
-    "            fieldset.mindepth - p.depth,\n",
-    "            p.ddepth,\n",
+    "        p.dz -= vertical_speed * dt\n",
+    "        p.temp = fieldset.thetao[p.time, p.z, p.lat, p.lon]\n",
+    "        p.cycle_phase = np.where(p.z + p.dz <= fieldset.mindepth, 4, p.cycle_phase)\n",
+    "        p.dz = np.where(\n",
+    "            p.z + p.dz <= fieldset.mindepth,\n",
+    "            fieldset.mindepth - p.z,\n",
+    "            p.dz,\n",
     "        )\n",
     "\n",
     "    RisingPhase(particles[particles.cycle_phase == 3])\n",
@@ -163,7 +157,7 @@
     "    pclass=ArgoParticle,\n",
     "    lon=[32],\n",
     "    lat=[-31],\n",
-    "    depth=[fieldset.mindepth],\n",
+    "    z=[fieldset.mindepth],\n",
     ")\n",
     "\n",
     "# combine Argo vertical movement kernel with built-in Advection kernel\n",
@@ -174,7 +168,7 @@
     "    ArgoPhase4,\n",
     "    ArgoPhase5,\n",
     "    ArgoPhase6,\n",
-    "    parcels.AdvectionRK4,\n",
+    "    parcels.kernels.AdvectionRK4,\n",
     "]\n",
     "\n",
     "# Create a ParticleFile object to store the output\n",
@@ -209,9 +203,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds_out = xr.open_zarr(\n",
-    "    output_file.store, decode_times=False\n",
-    ")  # TODO fix without using decode_times=False\n",
+    "ds_out = xr.open_zarr(output_file.store)\n",
     "x = ds_out[\"lon\"][:].squeeze()\n",
     "y = ds_out[\"lat\"][:].squeeze()\n",
     "z = ds_out[\"z\"][:].squeeze()\n",
@@ -268,7 +260,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "parcels-v4",
+   "display_name": "test-notebooks",
    "language": "python",
    "name": "python3"
   },