Move homepage animation to markdown format

Author: erikvansebille

docs/user_guide/examples/documentation_homepage_animation.ipynb

@@ -0,0 +1,150 @@
+# 🎓 The homepage animation
+
+This notebook shows how to create the animation on the homepage of the Parcels documentation. It uses a dataset of virtual particles at the surface of the global ocean simulation that can be retrieved from the [Copernicus Marine Service](https://marine.copernicus.eu/).
+
+```python
+import cartopy
+import cartopy.crs as ccrs
+import matplotlib.gridspec as gridspec
+import matplotlib.pyplot as plt
+import numpy as np
+import polars as pl
+import xarray as xr
+from matplotlib.animation import FuncAnimation, PillowWriter
+
+import parcels
+```
+
+The cell below provides the code needed to run this simulation - but because it is a time-consuming run (~20 minutes) and requires a login on the Copernicus Marine Service, we also provide the output file for download [here](https://github.com/Parcels-code/parcels-data/raw/refs/heads/main/data-parquet/copernicusmarine_globalsurface.parquet).
+
+```python
+particle_filename = "copernicusmarine_globalsurface.parquet"
+
+
+def run_global_copernicusmarine():
+    import copernicusmarine
+    copernicusmarine.login()
+
+    ds = copernicusmarine.open_dataset(
+        dataset_id="cmems_mod_glo_phy-cur_anfc_0.083deg_P1D-m",
+        variables=["uo", "vo"],
+        start_datetime="2024-01-01",
+        end_datetime="2024-12-31",
+        minimum_depth=0.5,
+        maximum_depth=0.5,
+        service="arco-geo-series",
+        chunk_size_limit=1,
+    )
+    ds = ds.fillna(0)
+
+    ds_wrap = xr.concat(
+        [
+            ds,
+            ds.isel(longitude=slice(0, 1)).assign_coords(
+                longitude=ds.longitude.isel(longitude=slice(0, 1)) + 360
+            ),
+        ],
+        dim="longitude",
+    )
+    ds = parcels.convert.copernicusmarine_to_sgrid(
+        fields={"U": ds_wrap["uo"], "V": ds_wrap["vo"]}
+    )
+    fieldset = parcels.FieldSet.from_sgrid_conventions(ds)
+    fieldset.UV.interp_method = parcels.interpolators.XFreeslip()
+    fieldset.to_windowed_arrays()
+
+    lon, lat = np.meshgrid(np.arange(-179, 180, 2), np.arange(-89, 90, 2))
+    lon = lon.flatten()
+    lat = lat.flatten()
+
+    # Filter out particles that are not in the ocean (i.e. where speed is zero)
+    u, v = fieldset.UV[np.zeros_like(lon), np.zeros_like(lat), lat, lon]
+    speed = np.sqrt(u**2 + v**2)
+    inocean = speed > 0
+
+    pset = parcels.ParticleSet(fieldset, x=lon[inocean], y=lat[inocean])
+
+    oufile = parcels.ParticleFile(
+        particle_filename,
+        outputdt=np.timedelta64(5, "D"),
+    )
+
+    def AdvectionRK2_periodic(particles, fieldset):  # pragma: no cover
+        """Advection of particles using second-order Runge-Kutta integration,
+        keeping particles within the periodic domain [-180, 180].
+        """
+        (u1, v1) = fieldset.UV[particles]
+        x1 = particles.x + u1 * 0.5 * particles.dt
+        x1 = ((x1 + 180) % 360) - 180
+        y1 = particles.y + v1 * 0.5 * particles.dt
+        (u2, v2) = fieldset.UV[
+            particles.t + 0.5 * particles.dt, particles.z, y1, x1, particles
+        ]
+        particles.dx += u2 * particles.dt
+        particles.dx = ((particles.dx + particles.x + 180) % 360) - (particles.x + 180)
+        particles.dy += v2 * particles.dt
+
+    pset.execute(
+        [AdvectionRK2_periodic],
+        dt=np.timedelta64(1, "h"),
+        runtime=np.timedelta64(365, "D"),
+        output_file=oufile,
+    )
+
+
+run_global_copernicusmarine()
+```
+
+The animation consists of two figures: the northern hemisphere and the southern hemisphere, using the [Cartopy package](https://cartopy.readthedocs.io/stable/) for map projections.
+
+```python
+fig = plt.figure(figsize=(8, 4))
+gs = gridspec.GridSpec(ncols=8, nrows=4, figure=fig)
+
+scat = [None, None]
+particles = df.filter(pl.col("t") == pl.lit(plottimes[0]))
+
+for i, central_latitude in enumerate([90, -90]):
+    ax = fig.add_subplot(
+        gs[:, :4] if central_latitude == 90 else gs[:, 4:],
+        projection=ccrs.NearsidePerspective(
+            central_latitude=central_latitude,
+            central_longitude=-30,
+            satellite_height=15000000,
+        ),
+    )
+    ax.add_feature(cartopy.feature.LAND, zorder=1)
+    ax.add_feature(cartopy.feature.OCEAN, zorder=1)
+    ax.coastlines()
+    scat[i] = ax.scatter(
+        particles["x"],
+        particles["y"],
+        marker=".",
+        s=25,
+        c="#AB2200",
+        edgecolor="white",
+        linewidth=0.15,
+        transform=ccrs.PlateCarree(),
+    )
+
+
+def animate(i):
+    particles = df.filter(pl.col("t") == pl.lit(plottimes[i]))
+    scat[0].set_offsets(np.c_[particles["x"], particles["y"]])
+    scat[1].set_offsets(np.c_[particles["x"], particles["y"]])
+    return scat[0], scat[1]
+
+
+plt.rcParams["animation.html"] = "jshtml"
+anim = FuncAnimation(fig, animate, frames=len(plottimes), interval=150, blit=True)
+plt.close(fig)
+anim.save(
+    particle_filename.replace(".parquet", ".gif"),
+    writer=PillowWriter(fps=6),
+    savefig_kwargs={"transparent": True},
+)
+```
+
+The resulting animation is then
+
+![gif](../../_static/homepage.gif)