refactor examples to import from parcels.kernels

docs/examples/documentation_advanced_zarr.ipynb

@@ -247,7 +247,7 @@
     "\n",
     "# run experiment\n",
     "pset.execute(\n",
-    "    parcels.AdvectionRK4,\n",
+    "    parcels.kernels.AdvectionRK4,\n",
     "    runtime=timedelta(days=17),\n",
     "    dt=timedelta(hours=3),\n",
     "    output_file=outputfile,\n",

docs/examples/documentation_geospatial.ipynb

@@ -172,7 +172,7 @@
     "\n",
     "\n",
     "pset.execute(\n",
-    "    [parcels.AdvectionRK4, DeleteParticle],\n",
+    "    [parcels.kernels.AdvectionRK4, DeleteParticle],\n",
     "    runtime=timedelta(days=120),\n",
     "    dt=dt,\n",
     "    output_file=output_file,\n",

docs/examples/documentation_stuck_particles.ipynb

@@ -454,7 +454,7 @@
     "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
-    "kernels = pset.Kernel(parcels.AdvectionRK4)\n",
+    "kernels = pset.Kernel(parcels.kernels.AdvectionRK4)\n",
     "\n",
     "output_file = pset.ParticleFile(name=\"SMOC.zarr\", outputdt=timedelta(hours=1))\n",
     "\n",
@@ -872,7 +872,7 @@
     "output_file = pset.ParticleFile(name=\"Cgrid-stuck.zarr\", outputdt=timedelta(hours=1))\n",
     "\n",
     "pset.execute(\n",
-    "    parcels.AdvectionRK4,\n",
+    "    parcels.kernels.AdvectionRK4,\n",
     "    runtime=timedelta(days=10),\n",
     "    dt=timedelta(minutes=5),\n",
     "    output_file=output_file,\n",
@@ -1182,8 +1182,8 @@
     "    name=\"Cgrid-diffusion.zarr\", outputdt=timedelta(hours=1)\n",
     ")\n",
     "pset.execute(\n",
-    "    pset.Kernel(parcels.AdvectionRK4)\n",
-    "    + pset.Kernel(parcels.DiffusionUniformKh)\n",
+    "    pset.Kernel(parcels.kernels.AdvectionRK4)\n",
+    "    + pset.Kernel(parcels.kernels.DiffusionUniformKh)\n",
     "    + pset.Kernel(Sample_land),\n",
     "    runtime=timedelta(days=10),\n",
     "    dt=timedelta(minutes=5),\n",

docs/examples/documentation_unstuck_Agrid.ipynb

@@ -852,7 +852,7 @@
     "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
-    "kernels = parcels.AdvectionRK4\n",
+    "kernels = parcels.kernels.AdvectionRK4\n",
     "\n",
     "output_file = pset.ParticleFile(name=\"SMOC.zarr\", outputdt=timedelta(hours=1))\n",
     "\n",
@@ -939,7 +939,7 @@
     "    fieldset=fieldset, pclass=DisplacementParticle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
-    "kernels = [displace, parcels.AdvectionRK4, set_displacement]\n",
+    "kernels = [displace, parcels.kernels.AdvectionRK4, set_displacement]\n",
     "\n",
     "output_file = pset.ParticleFile(name=\"SMOC-disp.zarr\", outputdt=timedelta(hours=1))\n",
     "\n",
@@ -1415,7 +1415,7 @@
     "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
-    "kernels = pset.Kernel(parcels.AdvectionRK4)\n",
+    "kernels = pset.Kernel(parcels.kernels.AdvectionRK4)\n",
     "\n",
     "output_file = pset.ParticleFile(\n",
     "    name=\"SMOC_partialslip.zarr\", outputdt=timedelta(hours=1)\n",
@@ -1452,7 +1452,7 @@
     "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
-    "kernels = pset.Kernel(parcels.AdvectionRK4)\n",
+    "kernels = pset.Kernel(parcels.kernels.AdvectionRK4)\n",
     "\n",
     "output_file = pset.ParticleFile(name=\"SMOC_freeslip.zarr\", outputdt=timedelta(hours=1))\n",
     "\n",

docs/examples/example_brownian.py

@@ -40,7 +40,9 @@ def test_brownian_example(mesh, npart=3000):
         lat=np.zeros(npart),
     )
     pset.execute(
-        pset.Kernel(parcels.DiffusionUniformKh), runtime=runtime, dt=timedelta(hours=1)
+        pset.Kernel(parcels.kernels.DiffusionUniformKh),
+        runtime=runtime,
+        dt=timedelta(hours=1),
     )
 
     expected_std_x = np.sqrt(2 * kh_zonal * runtime.total_seconds())

docs/examples/example_decaying_moving_eddy.py

@@ -67,7 +67,7 @@ def true_values(
     return np.array([x, y])
 
 
-def decaying_moving_example(fieldset, outfile, method=parcels.AdvectionRK4):
+def decaying_moving_example(fieldset, outfile, method=parcels.kernels.AdvectionRK4):
     pset = parcels.ParticleSet(
         fieldset, pclass=parcels.Particle, lon=start_lon, lat=start_lat
     )

docs/examples/example_globcurrent.py

@@ -57,8 +57,8 @@ def test_globcurrent_fieldset_advancetime(dt, lonstart, latstart):
         psetsub[0].time_nextloop = fieldsetsub.U.grid.time[-1]
         psetall[0].time_nextloop = fieldsetall.U.grid.time[-1]
 
-    psetsub.execute(parcels.AdvectionRK4, runtime=timedelta(days=7), dt=dt)
-    psetall.execute(parcels.AdvectionRK4, runtime=timedelta(days=7), dt=dt)
+    psetsub.execute(parcels.kernels.AdvectionRK4, runtime=timedelta(days=7), dt=dt)
+    psetall.execute(parcels.kernels.AdvectionRK4, runtime=timedelta(days=7), dt=dt)
 
     assert abs(psetsub[0].lon - psetall[0].lon) < 1e-4
 
@@ -74,7 +74,7 @@ def test_globcurrent_particles():
     )
 
     pset.execute(
-        parcels.AdvectionRK4, runtime=timedelta(days=1), dt=timedelta(minutes=5)
+        parcels.kernels.AdvectionRK4, runtime=timedelta(days=1), dt=timedelta(minutes=5)
     )
 
     assert abs(pset[0].lon - 23.8) < 1
@@ -132,7 +132,9 @@ def test_globcurrent_time_extrapolation_error():
     )
     with pytest.raises(parcels.TimeExtrapolationError):
         pset.execute(
-            parcels.AdvectionRK4, runtime=timedelta(days=1), dt=timedelta(minutes=5)
+            parcels.kernels.AdvectionRK4,
+            runtime=timedelta(days=1),
+            dt=timedelta(minutes=5),
         )
 
 
@@ -179,13 +181,13 @@ def SampleP(particle, fieldset, time):  # pragma: no cover
     if with_starttime:
         with pytest.raises(parcels.TimeExtrapolationError):
             pset.execute(
-                pset.Kernel(parcels.AdvectionRK4) + SampleP,
+                pset.Kernel(parcels.kernels.AdvectionRK4) + SampleP,
                 runtime=timedelta(days=1),
                 dt=dt,
             )
     else:
         pset.execute(
-            pset.Kernel(parcels.AdvectionRK4) + SampleP,
+            pset.Kernel(parcels.kernels.AdvectionRK4) + SampleP,
             runtime=timedelta(days=1),
             dt=dt,
         )
@@ -204,7 +206,7 @@ def DeleteP0(particle, fieldset, time):  # pragma: no cover
     )
 
     pset0.execute(
-        pset0.Kernel(DeleteP0) + parcels.AdvectionRK4,
+        pset0.Kernel(DeleteP0) + parcels.kernels.AdvectionRK4,
         runtime=timedelta(days=rundays),
         dt=timedelta(minutes=5),
     )
@@ -214,7 +216,9 @@ def DeleteP0(particle, fieldset, time):  # pragma: no cover
     )
 
     pset1.execute(
-        parcels.AdvectionRK4, runtime=timedelta(days=rundays), dt=timedelta(minutes=5)
+        parcels.kernels.AdvectionRK4,
+        runtime=timedelta(days=rundays),
+        dt=timedelta(minutes=5),
     )
 
     assert np.allclose([pset0[-1].lon, pset0[-1].lat], [pset1[-1].lon, pset1[-1].lat])
@@ -230,7 +234,10 @@ def test_globcurrent_pset_fromfile(dt, pid_offset, tmpdir):
     pset = parcels.ParticleSet(fieldset, pclass=parcels.Particle, lon=25, lat=-35)
     pfile = pset.ParticleFile(filename, outputdt=timedelta(hours=6))
     pset.execute(
-        parcels.AdvectionRK4, runtime=timedelta(days=1), dt=dt, output_file=pfile
+        parcels.kernels.AdvectionRK4,
+        runtime=timedelta(days=1),
+        dt=dt,
+        output_file=pfile,
     )
     pfile.write_latest_locations(pset, max(pset.time_nextloop))
 
@@ -241,8 +248,8 @@ def test_globcurrent_pset_fromfile(dt, pid_offset, tmpdir):
         filename=filename,
         restarttime=restarttime,
     )
-    pset.execute(parcels.AdvectionRK4, runtime=timedelta(days=1), dt=dt)
-    pset_new.execute(parcels.AdvectionRK4, runtime=timedelta(days=1), dt=dt)
+    pset.execute(parcels.kernels.AdvectionRK4, runtime=timedelta(days=1), dt=dt)
+    pset_new.execute(parcels.kernels.AdvectionRK4, runtime=timedelta(days=1), dt=dt)
 
     for var in ["lon", "lat", "depth", "time", "trajectory"]:
         assert np.allclose(

docs/examples/example_mitgcm.py

@@ -45,7 +45,7 @@ def periodicBC(particle, fieldset, time):  # pragma: no cover
         outputdt=timedelta(days=1),
         chunks=(len(pset), 1),
     )
-    kernels = parcels.AdvectionRK4 + pset.Kernel(periodicBC)
+    kernels = parcels.kernels.AdvectionRK4 + pset.Kernel(periodicBC)
     pset.execute(
         kernels, runtime=timedelta(days=5), dt=timedelta(minutes=30), output_file=pfile
     )

docs/examples/example_moving_eddies.py

@@ -8,9 +8,9 @@
 import parcels
 
 method = {
-    "RK4": parcels.AdvectionRK4,
-    "EE": parcels.AdvectionEE,
-    "RK45": parcels.AdvectionRK45,
+    "RK4": parcels.kernels.AdvectionRK4,
+    "EE": parcels.kernels.AdvectionEE,
+    "RK45": parcels.kernels.AdvectionRK45,
 }
 
 
@@ -112,7 +112,7 @@ def cosd(x):
 
 
 def moving_eddies_example(
-    fieldset, outfile, npart=2, verbose=False, method=parcels.AdvectionRK4
+    fieldset, outfile, npart=2, verbose=False, method=parcels.kernels.AdvectionRK4
 ):
     """Configuration of a particle set that follows two moving eddies.
 
@@ -161,7 +161,7 @@ def moving_eddies_example(
 
 @pytest.mark.parametrize("mesh", ["flat", "spherical"])
 def test_moving_eddies_fwdbwd(mesh, tmpdir, npart=2):
-    method = parcels.AdvectionRK4
+    method = parcels.kernels.AdvectionRK4
     fieldset = moving_eddies_fieldset(mesh=mesh)
 
     lons = [3.3, 3.3] if fieldset.U.grid.mesh == "spherical" else [3.3e5, 3.3e5]
@@ -284,7 +284,9 @@ def slowlySouthWestward(particle, fieldset, time):  # pragma: no cover
         particle.dlon -= 5 * particle.dt / 1e5
         particle.dlat -= 3 * particle.dt / 1e5
 
-    kernels = pset.Kernel(parcels.AdvectionRK4) + slowlySouthWestward + periodicBC
+    kernels = (
+        pset.Kernel(parcels.kernels.AdvectionRK4) + slowlySouthWestward + periodicBC
+    )
     pset.execute(kernels, runtime=timedelta(days=6), dt=timedelta(hours=1))
 
 

docs/examples/example_nemo_curvilinear.py

@@ -8,7 +8,10 @@
 
 import parcels
 
-advection = {"RK4": parcels.AdvectionRK4, "AA": parcels.AdvectionAnalytical}
+advection = {
+    "RK4": parcels.kernels.AdvectionRK4,
+    "AA": parcels.kernels.AdvectionAnalytical,
+}
 
 
 def run_nemo_curvilinear(outfile, advtype="RK4"):

docs/examples/example_ofam.py

@@ -51,12 +51,12 @@ def test_ofam_xarray_vs_netcdf(dt):
     psetN = parcels.ParticleSet(
         fieldsetNetcdf, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
-    psetN.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
+    psetN.execute(parcels.kernels.AdvectionRK4, runtime=runtime, dt=dt)
 
     psetX = parcels.ParticleSet(
         fieldsetxarray, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
-    psetX.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
+    psetX.execute(parcels.kernels.AdvectionRK4, runtime=runtime, dt=dt)
 
     assert np.allclose(psetN[0].lon, psetX[0].lon)
     assert np.allclose(psetN[0].lat, psetX[0].lat)
@@ -80,7 +80,9 @@ def test_ofam_particles(use_xarray):
     )
 
     pset.execute(
-        parcels.AdvectionRK4, runtime=timedelta(days=10), dt=timedelta(minutes=5)
+        parcels.kernels.AdvectionRK4,
+        runtime=timedelta(days=10),
+        dt=timedelta(minutes=5),
     )
 
     assert abs(pset[0].lon - 173) < 1

docs/examples/example_peninsula.py

@@ -8,9 +8,9 @@
 import parcels
 
 method = {
-    "RK4": parcels.AdvectionRK4,
-    "EE": parcels.AdvectionEE,
-    "RK45": parcels.AdvectionRK45,
+    "RK4": parcels.kernels.AdvectionRK4,
+    "EE": parcels.kernels.AdvectionEE,
+    "RK45": parcels.kernels.AdvectionRK45,
 }
 
 
@@ -102,7 +102,7 @@ def peninsula_example(
     degree=1,
     verbose=False,
     output=True,
-    method=parcels.AdvectionRK4,
+    method=parcels.kernels.AdvectionRK4,
 ):
     """Example configuration of particle flow around an idealised Peninsula
 
@@ -199,7 +199,7 @@ def test_peninsula_fieldset_AnalyticalAdvection(mesh, tmpdir):
     fieldset = peninsula_fieldset(101, 51, "flat", grid_type="C")
     outfile = tmpdir.join("PeninsulaAA")
     pset = peninsula_example(
-        fieldset, outfile, npart=10, method=parcels.AdvectionAnalytical
+        fieldset, outfile, npart=10, method=parcels.kernels.AdvectionAnalytical
     )
     # Test advection accuracy by comparing streamline values
     err_adv = np.array([abs(p.p_start - p.p) for p in pset])

docs/examples/example_radial_rotation.py

@@ -47,7 +47,7 @@ def true_values(age):  # Calculate the expected values for particle 2 at the end
     return [x, y]
 
 
-def rotation_example(fieldset, outfile, method=parcels.AdvectionRK4):
+def rotation_example(fieldset, outfile, method=parcels.kernels.AdvectionRK4):
     npart = 2  # Test two particles on the rotating fieldset.
     pset = parcels.ParticleSet.from_line(
         fieldset,

docs/examples/example_stommel.py

@@ -8,9 +8,9 @@
 import parcels
 
 method = {
-    "RK4": parcels.AdvectionRK4,
-    "EE": parcels.AdvectionEE,
-    "RK45": parcels.AdvectionRK45,
+    "RK4": parcels.kernels.AdvectionRK4,
+    "EE": parcels.kernels.AdvectionEE,
+    "RK45": parcels.kernels.AdvectionRK45,
 }
 
 
@@ -96,7 +96,7 @@ def simple_partition_function(coords, mpi_size=1):
 def stommel_example(
     npart=1,
     verbose=False,
-    method=parcels.AdvectionRK4,
+    method=parcels.kernels.AdvectionRK4,
     grid_type="A",
     outfile="StommelParticle.zarr",
     repeatdt=None,

docs/examples/parcels_tutorial.ipynb

@@ -217,7 +217,7 @@
    "outputs": [],
    "source": [
     "pset.execute(\n",
-    "    parcels.AdvectionRK4,  # the kernel (which defines how particles move)\n",
+    "    parcels.kernels.AdvectionRK4,  # the kernel (which defines how particles move)\n",
     "    runtime=timedelta(days=6),  # the total length of the run\n",
     "    dt=timedelta(minutes=5),  # the timestep of the kernel\n",
     "    output_file=output_file,\n",
@@ -361,7 +361,7 @@
     "    outputdt=timedelta(hours=1),  # the time step of the outputs\n",
     ")\n",
     "pset.execute(\n",
-    "    parcels.AdvectionRK4,\n",
+    "    parcels.kernels.AdvectionRK4,\n",
     "    dt=-timedelta(minutes=5),  # negative timestep for backward run\n",
     "    runtime=timedelta(days=6),  # the run time\n",
     "    output_file=output_file,\n",
@@ -461,7 +461,7 @@
     "    name=\"EddyParticles_WestVel.zarr\", outputdt=timedelta(hours=1)\n",
     ")\n",
     "pset.execute(\n",
-    "    [parcels.AdvectionRK4, WestVel],  # simply combine the Kernels in a list\n",
+    "    [parcels.kernels.AdvectionRK4, WestVel],  # simply combine the Kernels in a list\n",
     "    runtime=timedelta(days=2),\n",
     "    dt=timedelta(minutes=5),\n",
     "    output_file=output_file,\n",
@@ -615,7 +615,7 @@
     "    name=\"GlobCurrentParticles.zarr\", outputdt=timedelta(hours=6)\n",
     ")\n",
     "pset.execute(\n",
-    "    parcels.AdvectionRK4,\n",
+    "    parcels.kernels.AdvectionRK4,\n",
     "    runtime=timedelta(days=10),\n",
     "    dt=timedelta(minutes=5),\n",
     "    output_file=output_file,\n",
@@ -770,7 +770,7 @@
     "    name=\"PeninsulaPressure.zarr\", outputdt=timedelta(hours=1)\n",
     ")\n",
     "pset.execute(\n",
-    "    [parcels.AdvectionRK4, SampleP],  # list of kernels to be executed\n",
+    "    [parcels.kernels.AdvectionRK4, SampleP],  # list of kernels to be executed\n",
     "    runtime=timedelta(hours=20),\n",
     "    dt=timedelta(minutes=5),\n",
     "    output_file=output_file,\n",
@@ -936,7 +936,7 @@
    "outputs": [],
    "source": [
     "pset.execute(\n",
-    "    [parcels.AdvectionRK4, TotalDistance],  # list of kernels to be executed\n",
+    "    [parcels.kernels.AdvectionRK4, TotalDistance],  # list of kernels to be executed\n",
     "    runtime=timedelta(days=6),\n",
     "    dt=timedelta(minutes=5),\n",
     "    output_file=pset.ParticleFile(\n",