Second batch of tutorial cleanups after #2719

Author: erikvansebille

docs/user_guide/examples/tutorial_interaction.ipynb

@@ -63,12 +63,12 @@
     "\n",
     "    # Boolean mask and coordinates of attractors\n",
     "    attractor_mask = particles.attractor.astype(bool)\n",
-    "    lon_a = particles.lon[attractor_mask]\n",
-    "    lat_a = particles.lat[attractor_mask]\n",
+    "    x_a = particles.x[attractor_mask]\n",
+    "    y_a = particles.y[attractor_mask]\n",
     "\n",
     "    # Pairwise differences and distances (n_attractors × n_particles)\n",
-    "    dx = particles.lon - lon_a[:, None]\n",
-    "    dy = particles.lat - lat_a[:, None]\n",
+    "    dx = particles.x - x_a[:, None]\n",
+    "    dy = particles.y - y_a[:, None]\n",
     "    distances = np.sqrt(dx**2 + dy**2)\n",
     "\n",
     "    # Mask dx, dy by interaction range\n",
@@ -81,8 +81,8 @@
     "        dx_norm = dx * inv_dist\n",
     "        dy_norm = dy * inv_dist\n",
     "\n",
-    "    particles.dlon += np.sum(dx_norm, axis=0) * velocity * particles.dt\n",
-    "    particles.dlat += np.sum(dy_norm, axis=0) * velocity * particles.dt"
+    "    particles.dx += np.sum(dx_norm, axis=0) * velocity * particles.dt\n",
+    "    particles.dy += np.sum(dy_norm, axis=0) * velocity * particles.dt"
    ]
   },
   {
@@ -124,8 +124,8 @@
     "pset = parcels.ParticleSet(\n",
     "    fieldset=DiffusionFieldSet(),\n",
     "    pclass=InteractingParticle,\n",
-    "    lon=X,\n",
-    "    lat=Y,\n",
+    "    x=X,\n",
+    "    y=Y,\n",
     "    attractor=attractor,\n",
     ")\n",
     "\n",
@@ -170,17 +170,17 @@
     "ax.set_ylim(-1.1, 1.1)\n",
     "\n",
     "particles = df_other.filter(pl.col(\"time\") == pl.lit(timerange[0]))\n",
-    "scatter = ax.scatter(particles[\"lon\"], particles[\"lat\"], c=\"b\", s=5, zorder=1)\n",
+    "scatter = ax.scatter(particles[\"x\"], particles[\"y\"], c=\"b\", s=5, zorder=1)\n",
     "particles_attr = df_attr.filter(pl.col(\"time\") == pl.lit(timerange[0]))\n",
     "scatter_attr = ax.scatter(\n",
-    "    particles_attr[\"lon\"], particles_attr[\"lat\"], c=\"r\", s=40, zorder=2\n",
+    "    particles_attr[\"x\"], particles_attr[\"y\"], c=\"r\", s=40, zorder=2\n",
     ")\n",
     "circs = []\n",
-    "for lon_a, lat_a in zip(particles_attr[\"lon\"], particles_attr[\"lat\"], strict=True):\n",
+    "for x_a, y_a in zip(particles_attr[\"x\"], particles_attr[\"y\"], strict=True):\n",
     "    circs.append(\n",
     "        ax.add_patch(\n",
     "            plt.Circle(\n",
-    "                (lon_a, lat_a), 0.25, facecolor=\"None\", edgecolor=\"r\", linestyle=\"--\"\n",
+    "                (x_a, y_a), 0.25, facecolor=\"None\", edgecolor=\"r\", linestyle=\"--\"\n",
     "            )\n",
     "        )\n",
     "    )\n",
@@ -192,13 +192,13 @@
     "\n",
     "def animate(i):\n",
     "    particles = df_other.filter(pl.col(\"time\") == pl.lit(timerange[i]))\n",
-    "    scatter.set_offsets(np.c_[particles[\"lon\"], particles[\"lat\"]])\n",
+    "    scatter.set_offsets(np.c_[particles[\"x\"], particles[\"y\"]])\n",
     "    particles_attr = df_attr.filter(pl.col(\"time\") == pl.lit(timerange[i]))\n",
-    "    scatter_attr.set_offsets(np.c_[particles_attr[\"lon\"], particles_attr[\"lat\"]])\n",
-    "    for c, lon_a, lat_a in zip(\n",
-    "        circs, particles_attr[\"lon\"], particles_attr[\"lat\"], strict=True\n",
+    "    scatter_attr.set_offsets(np.c_[particles_attr[\"x\"], particles_attr[\"y\"]])\n",
+    "    for c, x_a, y_a in zip(\n",
+    "        circs, particles_attr[\"x\"], particles_attr[\"y\"], strict=True\n",
     "    ):\n",
-    "        c.center = (lon_a, lat_a)\n",
+    "        c.center = (x_a, y_a)\n",
     "    title.set_text(\n",
     "        f\"Particles at t = {timerange[i].total_seconds()}s\\n(Red particles are attractors)\"\n",
     "    )\n",
@@ -235,11 +235,11 @@
     "    \"\"\"\n",
     "    interaction_distance = 0.05\n",
     "\n",
-    "    N = len(particles.lon)\n",
+    "    N = len(particles.x)\n",
     "\n",
     "    # calculate pairwise distances (n_particles × n_particles)\n",
-    "    dx = particles.lon[None, :] - particles.lon[:, None]\n",
-    "    dy = particles.lat[None, :] - particles.lat[:, None]\n",
+    "    dx = particles.x[None, :] - particles.x[:, None]\n",
+    "    dy = particles.y[None, :] - particles.y[:, None]\n",
     "    distances = np.sqrt(dx**2 + dy**2)\n",
     "\n",
     "    # mask distances by interaction range\n",
@@ -291,8 +291,8 @@
     "pset = parcels.ParticleSet(\n",
     "    fieldset=DiffusionFieldSet(),\n",
     "    pclass=MergeParticle,\n",
-    "    lon=np.random.uniform(-1, 1, size=npart),\n",
-    "    lat=np.random.uniform(-1, 1, size=npart),\n",
+    "    x=np.random.uniform(-1, 1, size=npart),\n",
+    "    y=np.random.uniform(-1, 1, size=npart),\n",
     "    mass=np.random.uniform(0.5, 1.5, size=npart),\n",
     ")\n",
     "\n",
@@ -335,14 +335,14 @@
     "\n",
     "particles = df.filter(pl.col(\"time\") == pl.lit(timerange[0]))\n",
     "scatter = ax.scatter(\n",
-    "    particles[\"lon\"], particles[\"lat\"], c=\"b\", s=particles[\"mass\"], zorder=1\n",
+    "    particles[\"x\"], particles[\"y\"], c=\"b\", s=particles[\"mass\"], zorder=1\n",
     ")\n",
     "title = ax.set_title(f\"Particles at t = {timerange[0].total_seconds()}s\")\n",
     "\n",
     "\n",
     "def animate(i):\n",
     "    particles = df.filter(pl.col(\"time\") == pl.lit(timerange[i]))\n",
-    "    scatter.set_offsets(np.c_[particles[\"lon\"], particles[\"lat\"]])\n",
+    "    scatter.set_offsets(np.c_[particles[\"x\"], particles[\"y\"]])\n",
     "    scatter.set_sizes(particles[\"mass\"])\n",
     "    title.set_text(f\"Particles at t = {timerange[i].total_seconds()}s\")\n",
     "\n",
@@ -355,7 +355,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "docs",
+   "display_name": "Parcels:docs (3.14.6)",
    "language": "python",
    "name": "python3"
   },
@@ -369,7 +369,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.4"
+   "version": "3.14.6"
   }
  },
  "nbformat": 4,

docs/user_guide/examples/tutorial_interpolation.ipynb

@@ -133,7 +133,7 @@
     "    print(fieldset.P.interp_method.__class__.__name__)\n",
     "    xv, yv = np.meshgrid(np.linspace(0, 1, 8), np.linspace(0, 1, 8))\n",
     "    pset[p_interp.__class__.__name__] = parcels.ParticleSet(\n",
-    "        fieldset, pclass=SampleParticle, lon=xv.flatten(), lat=yv.flatten()\n",
+    "        fieldset, pclass=SampleParticle, x=xv.flatten(), y=yv.flatten()\n",
     "    )\n",
     "    pset[p_interp.__class__.__name__].execute(\n",
     "        SampleP,\n",
@@ -170,7 +170,7 @@
     "            ax[i].axvline(lon, color=\"k\", linestyle=\"--\")\n",
     "    pc = ax[i].pcolormesh(x, y, data, vmin=0.1, vmax=1.1)\n",
     "    ax[i].scatter(\n",
-    "        pset[p].lon, pset[p].lat, c=pset[p].p, edgecolors=\"k\", s=50, vmin=0.1, vmax=1.1\n",
+    "        pset[p].x, pset[p].y, c=pset[p].p, edgecolors=\"k\", s=50, vmin=0.1, vmax=1.1\n",
     "    )\n",
     "    xp, yp = np.meshgrid(fieldset.P.grid.lon, fieldset.P.grid.lat)\n",
     "    ax[i].plot(xp, yp, \"kx\")\n",
@@ -198,8 +198,8 @@
    "outputs": [],
    "source": [
     "plt.scatter(\n",
-    "    pset[\"XLinear\"].lon,\n",
-    "    pset[\"XLinear\"].lat,\n",
+    "    pset[\"XLinear\"].x,\n",
+    "    pset[\"XLinear\"].y,\n",
     "    c=pset[\"XLinearInvdistLandTracer\"].p - pset[\"XLinear\"].p,\n",
     "    edgecolors=\"k\",\n",
     "    s=50,\n",
@@ -339,7 +339,7 @@
     "xv, yv = np.meshgrid(np.linspace(0.2, 0.8, 8), np.linspace(0.2, 0.9, 8))\n",
     "\n",
     "pset[\"node\"] = parcels.ParticleSet(\n",
-    "    fieldset, pclass=SampleParticle, lon=xv.flatten(), lat=yv.flatten()\n",
+    "    fieldset, pclass=SampleParticle, x=xv.flatten(), y=yv.flatten()\n",
     ")\n",
     "pset[\"node\"].execute(\n",
     "    SampleTracer_Node,\n",
@@ -349,7 +349,7 @@
     ")\n",
     "\n",
     "pset[\"face\"] = parcels.ParticleSet(\n",
-    "    fieldset, pclass=SampleParticle, lon=xv.flatten(), lat=yv.flatten()\n",
+    "    fieldset, pclass=SampleParticle, x=xv.flatten(), y=yv.flatten()\n",
     ")\n",
     "pset[\"face\"].execute(\n",
     "    SampleTracer_Face,\n",
@@ -403,8 +403,8 @@
     ")\n",
     "\n",
     "ax[0].scatter(\n",
-    "    pset[\"node\"].lon,\n",
-    "    pset[\"node\"].lat,\n",
+    "    pset[\"node\"].x,\n",
+    "    pset[\"node\"].y,\n",
     "    c=pset[\"node\"].tracer,\n",
     "    cmap=\"viridis\",\n",
     "    edgecolors=\"k\",\n",
@@ -442,8 +442,8 @@
     "yf = ds.uxgrid.face_lat.values\n",
     "\n",
     "ax[1].scatter(\n",
-    "    pset[\"face\"].lon,\n",
-    "    pset[\"face\"].lat,\n",
+    "    pset[\"face\"].x,\n",
+    "    pset[\"face\"].y,\n",
     "    c=pset[\"face\"].tracer,\n",
     "    cmap=\"viridis\",\n",
     "    edgecolors=\"k\",\n",

docs/user_guide/examples/tutorial_nemo.ipynb

@@ -149,7 +149,7 @@
     "latp = np.linspace(-70, 88, npart)\n",
     "runtime = np.timedelta64(40, \"D\")\n",
     "\n",
-    "pset = parcels.ParticleSet(fieldset, lon=lonp, lat=latp)\n",
+    "pset = parcels.ParticleSet(fieldset, x=lonp, y=latp)\n",
     "pfile = parcels.ParticleFile(\n",
     "    \"output_curvilinear.parquet\", outputdt=np.timedelta64(1, \"D\")\n",
     ")\n",
@@ -160,7 +160,7 @@
     "    dt=np.timedelta64(1, \"D\"),\n",
     "    output_file=pfile,\n",
     ")\n",
-    "np.testing.assert_allclose(pset.lat, latp, atol=1e-1)"
+    "np.testing.assert_allclose(pset.y, latp, atol=1e-1)"
    ]
   },
   {
@@ -179,7 +179,7 @@
     "df = parcels.read_particlefile(\"output_curvilinear.parquet\")\n",
     "\n",
     "for traj in df.partition_by(\"particle_id\", maintain_order=True):\n",
-    "    plt.plot(traj[\"lon\"], traj[\"lat\"], \".-\")\n",
+    "    plt.plot(traj[\"x\"], traj[\"y\"], \".-\")\n",
     "\n",
     "plt.vlines(np.arange(-180, 901, 360), -90, 90, color=\"r\", label=\"antimeridian\")\n",
     "plt.ylabel(\"Latitude [deg N]\")\n",
@@ -204,12 +204,12 @@
    "outputs": [],
    "source": [
     "# post processing\n",
-    "df = df.with_columns((pl.col(\"lon\") % 360).alias(\"lon\"))\n",
+    "df = df.with_columns((pl.col(\"x\") % 360).alias(\"x\"))\n",
     "df = df.with_columns(\n",
-    "    pl.when(pl.col(\"lon\") <= 180)\n",
-    "    .then(pl.col(\"lon\"))\n",
-    "    .otherwise(pl.col(\"lon\") - 360)\n",
-    "    .alias(\"lon\")\n",
+    "    pl.when(pl.col(\"x\") <= 180)\n",
+    "    .then(pl.col(\"x\"))\n",
+    "    .otherwise(pl.col(\"x\") - 360)\n",
+    "    .alias(\"x\")\n",
     ")"
    ]
   },
@@ -225,12 +225,12 @@
    "source": [
     "# with a Kernel\n",
     "def periodicBC(particles, fieldset):  # pragma: no cover\n",
-    "    particles.dlon = np.where(\n",
-    "        particles.lon + particles.dlon > 180, particles.dlon - 360, particles.dlon\n",
+    "    particles.dx = np.where(\n",
+    "        particles.x + particles.dx > 180, particles.dx - 360, particles.dx\n",
     "    )\n",
     "\n",
     "\n",
-    "pset = parcels.ParticleSet(fieldset, lon=lonp, lat=latp)\n",
+    "pset = parcels.ParticleSet(fieldset, x=lonp, y=latp)\n",
     "pfile = parcels.ParticleFile(\n",
     "    \"output_curvilinear_periodic.parquet\", outputdt=np.timedelta64(1, \"D\")\n",
     ")\n",
@@ -251,7 +251,7 @@
    "source": [
     "fig, ax = plt.subplots(1, 2, figsize=(10, 5))\n",
     "for traj in df.partition_by(\"particle_id\", maintain_order=True):\n",
-    "    ax[0].plot(traj[\"lon\"], traj[\"lat\"], \".-\")\n",
+    "    ax[0].plot(traj[\"x\"], traj[\"y\"], \".-\")\n",
     "ax[0].vlines(np.arange(-180, 360, 360), -90, 90, color=\"r\", label=\"antimeridian\")\n",
     "ax[0].set_ylabel(\"Latitude [deg N]\")\n",
     "ax[0].set_xlabel(\"Longitude [deg E]\")\n",
@@ -262,7 +262,7 @@
     "\n",
     "df_periodic = parcels.read_particlefile(\"output_curvilinear_periodic.parquet\")\n",
     "for traj in df_periodic.partition_by(\"particle_id\", maintain_order=True):\n",
-    "    ax[1].plot(traj[\"lon\"], traj[\"lat\"], \".-\")\n",
+    "    ax[1].plot(traj[\"x\"], traj[\"y\"], \".-\")\n",
     "\n",
     "ax[1].vlines(np.arange(-180, 360, 360), -90, 90, color=\"r\", label=\"antimeridian\")\n",
     "ax[1].set_ylabel(\"Latitude [deg N]\")\n",
@@ -330,8 +330,8 @@
     "npart = 10\n",
     "pset = parcels.ParticleSet(\n",
     "    fieldset=fieldset,\n",
-    "    lon=np.linspace(1.9, 3.4, npart),\n",
-    "    lat=np.linspace(65, 51.6, npart),\n",
+    "    x=np.linspace(1.9, 3.4, npart),\n",
+    "    y=np.linspace(65, 51.6, npart),\n",
     "    z=100 * np.ones(npart),\n",
     ")\n",
     "\n",
@@ -366,17 +366,15 @@
     "vmin = df[\"z\"].min()\n",
     "vmax = df[\"z\"].max()\n",
     "for traj in df.partition_by(\"particle_id\", maintain_order=True):\n",
-    "    plt.scatter(\n",
-    "        traj[\"lon\"], traj[\"lat\"], c=-traj[\"z\"], marker=\".\", vmin=-vmax, vmax=-vmin\n",
-    "    )\n",
+    "    plt.scatter(traj[\"x\"], traj[\"y\"], c=-traj[\"z\"], marker=\".\", vmin=-vmax, vmax=-vmin)\n",
     "plt.colorbar(label=\"Depth (m)\")\n",
     "plt.show()"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "docs",
+   "display_name": "Parcels:docs (3.14.6)",
    "language": "python",
    "name": "python3"
   },
@@ -390,7 +388,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.4"
+   "version": "3.14.6"
   }
  },
  "nbformat": 4,