[#1861] Change ScipyParticle to Particle and ScipyInteractionParticle…

docs/examples/documentation_MPI.ipynb

@@ -245,7 +245,7 @@
     "    fieldset = set_cms_fieldset(cs)\n",
     "    pset = parcels.ParticleSet(\n",
     "        fieldset=fieldset,\n",
-    "        pclass=parcels.ScipyParticle,\n",
+    "        pclass=parcels.Particle,\n",
     "        lon=[0],\n",
     "        lat=[0],\n",
     "        repeatdt=timedelta(hours=1),\n",
@@ -400,7 +400,7 @@
     "    fieldset = set_cms_fieldset_3D(cs)\n",
     "    pset = parcels.ParticleSet(\n",
     "        fieldset=fieldset,\n",
-    "        pclass=parcels.ScipyParticle,\n",
+    "        pclass=parcels.Particle,\n",
     "        lon=[0],\n",
     "        lat=[0],\n",
     "        repeatdt=timedelta(hours=1),\n",

docs/examples/documentation_geospatial.ipynb

@@ -167,7 +167,7 @@
     "# Mesh of particles\n",
     "lons, lats = np.meshgrid(range(15, 35, 2), range(-40, -30, 2))\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lons, lat=lats\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats\n",
     ")\n",
     "dt = timedelta(hours=24)\n",
     "output_file = pset.ParticleFile(\n",

docs/examples/documentation_stuck_particles.ipynb

@@ -482,7 +482,7 @@
     "time = np.zeros(lons.size)\n",
     "\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lons, lat=lats, time=time\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
     "kernels = pset.Kernel(parcels.AdvectionRK4)\n",
@@ -940,7 +940,7 @@
     "time = np.zeros(npart)\n",
     "\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lon, lat=lat, time=time\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lon, lat=lat, time=time\n",
     ")\n",
     "\n",
     "output_file = pset.ParticleFile(name=\"Cgrid-stuck.zarr\", outputdt=timedelta(hours=1))\n",
@@ -1217,7 +1217,7 @@
    },
    "outputs": [],
    "source": [
-    "LandParticle = parcels.ScipyParticle.add_variable(\"on_land\")\n",
+    "LandParticle = parcels.Particle.add_variable(\"on_land\")\n",
     "\n",
     "\n",
     "def Sample_land(particle, fieldset, time):\n",

docs/examples/documentation_unstuck_Agrid.ipynb

@@ -799,7 +799,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "DisplacementParticle = parcels.ScipyParticle.add_variables(\n",
+    "DisplacementParticle = parcels.Particle.add_variables(\n",
     "    [\n",
     "        parcels.Variable(\"dU\"),\n",
     "        parcels.Variable(\"dV\"),\n",
@@ -902,7 +902,7 @@
    ],
    "source": [
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lons, lat=lats, time=time\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
     "kernels = parcels.AdvectionRK4\n",
@@ -1513,7 +1513,7 @@
     ")\n",
     "\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lons, lat=lats, time=time\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
     "kernels = pset.Kernel(parcels.AdvectionRK4)\n",
@@ -1559,7 +1559,7 @@
     "    },  # Setting the interpolation for U and V\n",
     ")\n",
     "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lons, lat=lats, time=time\n",
+    "    fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats, time=time\n",
     ")\n",
     "\n",
     "kernels = pset.Kernel(parcels.AdvectionRK4)\n",

docs/examples/example_brownian.py

@@ -35,7 +35,7 @@ def test_brownian_example(mesh, npart=3000):
     random.seed(1234)
     pset = parcels.ParticleSet(
         fieldset=fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=np.zeros(npart),
         lat=np.zeros(npart),
     )

docs/examples/example_decaying_moving_eddy.py

@@ -69,7 +69,7 @@ def true_values(
 
 def decaying_moving_example(fieldset, outfile, method=parcels.AdvectionRK4):
     pset = parcels.ParticleSet(
-        fieldset, pclass=parcels.ScipyParticle, lon=start_lon, lat=start_lat
+        fieldset, pclass=parcels.Particle, lon=start_lon, lat=start_lat
     )
 
     dt = timedelta(minutes=5)

docs/examples/example_globcurrent.py

@@ -75,7 +75,7 @@ def test_globcurrent_fieldset_advancetime(dt, lonstart, latstart, use_xarray):
     fieldsetsub = set_globcurrent_fieldset(files[0:10], use_xarray=use_xarray)
     psetsub = parcels.ParticleSet.from_list(
         fieldset=fieldsetsub,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=[lonstart],
         lat=[latstart],
     )
@@ -85,7 +85,7 @@ def test_globcurrent_fieldset_advancetime(dt, lonstart, latstart, use_xarray):
     )
     psetall = parcels.ParticleSet.from_list(
         fieldset=fieldsetall,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=[lonstart],
         lat=[latstart],
     )
@@ -107,7 +107,7 @@ def test_globcurrent_particles(use_xarray):
     latstart = [-35]
 
     pset = parcels.ParticleSet(
-        fieldset, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldset, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
 
     pset.execute(
@@ -126,7 +126,7 @@ def test_globcurrent_time_periodic(rundays):
             time_periodic=timedelta(days=365), deferred_load=deferred_load
         )
 
-        MyParticle = parcels.ScipyParticle.add_variable("sample_var", initial=0.0)
+        MyParticle = parcels.Particle.add_variable("sample_var", initial=0.0)
 
         pset = parcels.ParticleSet(
             fieldset, pclass=MyParticle, lon=25, lat=-35, time=fieldset.U.grid.time[0]
@@ -149,12 +149,12 @@ def test_globcurrent_xarray_vs_netcdf(dt):
     lonstart, latstart, runtime = (25, -35, timedelta(days=7))
 
     psetN = parcels.ParticleSet(
-        fieldsetNetcdf, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldsetNetcdf, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
     psetN.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
 
     psetX = parcels.ParticleSet(
-        fieldsetxarray, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldsetxarray, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
     psetX.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
 
@@ -170,12 +170,12 @@ def test_globcurrent_netcdf_timestamps(dt):
     lonstart, latstart, runtime = (25, -35, timedelta(days=7))
 
     psetN = parcels.ParticleSet(
-        fieldsetNetcdf, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldsetNetcdf, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
     psetN.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
 
     psetT = parcels.ParticleSet(
-        fieldsetTimestamps, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldsetTimestamps, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
     psetT.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
 
@@ -192,28 +192,28 @@ def test__particles_init_time():
     # tests the different ways of initialising the time of a particle
     pset = parcels.ParticleSet(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=lonstart,
         lat=latstart,
         time=np.datetime64("2002-01-15"),
     )
     pset2 = parcels.ParticleSet(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=lonstart,
         lat=latstart,
         time=14 * 86400,
     )
     pset3 = parcels.ParticleSet(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=lonstart,
         lat=latstart,
         time=np.array([np.datetime64("2002-01-15")]),
     )
     pset4 = parcels.ParticleSet(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=lonstart,
         lat=latstart,
         time=[np.datetime64("2002-01-15")],
@@ -228,7 +228,7 @@ def test_globcurrent_time_extrapolation_error(use_xarray):
     fieldset = set_globcurrent_fieldset(use_xarray=use_xarray)
     pset = parcels.ParticleSet(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=[25],
         lat=[-35],
         time=fieldset.U.grid.time[0] - timedelta(days=1).total_seconds(),
@@ -254,7 +254,7 @@ def test_globcurrent_startparticles_between_time_arrays(dt, with_starttime):
         )
     )
 
-    MyParticle = parcels.ScipyParticle.add_variable("sample_var", initial=0.0)
+    MyParticle = parcels.Particle.add_variable("sample_var", initial=0.0)
 
     def SampleP(particle, fieldset, time):  # pragma: no cover
         particle.sample_var += fieldset.P[
@@ -293,7 +293,7 @@ def DeleteP0(particle, fieldset, time):  # pragma: no cover
             particle.delete()
 
     pset0 = parcels.ParticleSet(
-        fieldset, pclass=parcels.ScipyParticle, lon=[25, 25], lat=[-35, -35], time=time0
+        fieldset, pclass=parcels.Particle, lon=[25, 25], lat=[-35, -35], time=time0
     )
 
     pset0.execute(
@@ -303,7 +303,7 @@ def DeleteP0(particle, fieldset, time):  # pragma: no cover
     )
 
     pset1 = parcels.ParticleSet(
-        fieldset, pclass=parcels.ScipyParticle, lon=[25, 25], lat=[-35, -35], time=time0
+        fieldset, pclass=parcels.Particle, lon=[25, 25], lat=[-35, -35], time=time0
     )
 
     pset1.execute(
@@ -319,8 +319,8 @@ def test_globcurrent_pset_fromfile(dt, pid_offset, tmpdir):
     filename = tmpdir.join("pset_fromparticlefile.zarr")
     fieldset = set_globcurrent_fieldset()
 
-    parcels.ScipyParticle.setLastID(pid_offset)
-    pset = parcels.ParticleSet(fieldset, pclass=parcels.ScipyParticle, lon=25, lat=-35)
+    parcels.Particle.setLastID(pid_offset)
+    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
@@ -330,7 +330,7 @@ def test_globcurrent_pset_fromfile(dt, pid_offset, tmpdir):
     restarttime = np.nanmax if dt > 0 else np.nanmin
     pset_new = parcels.ParticleSet.from_particlefile(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         filename=filename,
         restarttime=restarttime,
     )
@@ -351,7 +351,7 @@ def test_error_outputdt_not_multiple_dt(tmpdir):
 
     dt = 81.2584344538292  # number for which output writing fails
 
-    pset = parcels.ParticleSet(fieldset, pclass=parcels.ScipyParticle, lon=[0], lat=[0])
+    pset = parcels.ParticleSet(fieldset, pclass=parcels.Particle, lon=[0], lat=[0])
     ofile = pset.ParticleFile(name=filepath, outputdt=timedelta(days=1))
 
     def DoNothing(particle, fieldset, time):  # pragma: no cover

docs/examples/example_mitgcm.py

@@ -32,7 +32,7 @@ def periodicBC(particle, fieldset, time):  # pragma: no cover
     # Release particles 5 cells away from the Eastern boundary
     pset = parcels.ParticleSet.from_line(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         start=(fieldset.U.grid.lon[-5], fieldset.U.grid.lat[5]),
         finish=(fieldset.U.grid.lon[-5], fieldset.U.grid.lat[-5]),
         size=10,

docs/examples/example_moving_eddies.py

@@ -136,7 +136,7 @@ def moving_eddies_example(
     pset = parcels.ParticleSet.from_line(
         fieldset=fieldset,
         size=npart,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         start=start,
         finish=finish,
     )
@@ -168,7 +168,7 @@ def test_moving_eddies_fwdbwd(mesh, tmpdir, npart=2):
     lons = [3.3, 3.3] if fieldset.U.grid.mesh == "spherical" else [3.3e5, 3.3e5]
     lats = [46.0, 47.8] if fieldset.U.grid.mesh == "spherical" else [1e5, 2.8e5]
     pset = parcels.ParticleSet(
-        fieldset=fieldset, pclass=parcels.ScipyParticle, lon=lons, lat=lats
+        fieldset=fieldset, pclass=parcels.Particle, lon=lons, lat=lats
     )
 
     # Execte for 14 days, with 30sec timesteps and hourly output
@@ -262,7 +262,7 @@ def test_periodic_and_computeTimeChunk_eddies():
     fieldset.add_periodic_halo(zonal=True, meridional=True)
     pset = parcels.ParticleSet.from_list(
         fieldset=fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=[3.3, 3.3],
         lat=[46.0, 47.8],
     )

docs/examples/example_nemo_curvilinear.py

@@ -48,9 +48,7 @@ def periodicBC(particle, fieldSet, time):  # pragma: no cover
         if particle.lon > 180:
             particle_dlon -= 360  # noqa
 
-    pset = parcels.ParticleSet.from_list(
-        fieldset, parcels.ScipyParticle, lon=lonp, lat=latp
-    )
+    pset = parcels.ParticleSet.from_list(fieldset, parcels.Particle, lon=lonp, lat=latp)
     pfile = parcels.ParticleFile(outfile, pset, outputdt=timedelta(days=1))
     kernels = pset.Kernel(advection[advtype]) + periodicBC
     pset.execute(kernels, runtime=runtime, dt=timedelta(hours=6), output_file=pfile)

docs/examples/example_ofam.py

@@ -51,12 +51,12 @@ def test_ofam_xarray_vs_netcdf(dt):
     lonstart, latstart, runtime = (180, 10, timedelta(days=7))
 
     psetN = parcels.ParticleSet(
-        fieldsetNetcdf, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldsetNetcdf, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
     psetN.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
 
     psetX = parcels.ParticleSet(
-        fieldsetxarray, pclass=parcels.ScipyParticle, lon=lonstart, lat=latstart
+        fieldsetxarray, pclass=parcels.Particle, lon=lonstart, lat=latstart
     )
     psetX.execute(parcels.AdvectionRK4, runtime=runtime, dt=dt)
 
@@ -75,7 +75,7 @@ def test_ofam_particles(use_xarray):
 
     pset = parcels.ParticleSet(
         fieldset,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         lon=lonstart,
         lat=latstart,
         depth=depstart,

docs/examples/example_peninsula.py

@@ -127,7 +127,7 @@ def peninsula_example(
     """
     # First, we define a custom Particle class to which we add a
     # custom variable, the initial stream function value p.
-    MyParticle = parcels.ScipyParticle.add_variable(
+    MyParticle = parcels.Particle.add_variable(
         [
             parcels.Variable("p", dtype=np.float32, initial=0.0),
             parcels.Variable("p_start", dtype=np.float32, initial=0),

docs/examples/example_radial_rotation.py

@@ -52,7 +52,7 @@ def rotation_example(fieldset, outfile, method=parcels.AdvectionRK4):
     pset = parcels.ParticleSet.from_line(
         fieldset,
         size=npart,
-        pclass=parcels.ScipyParticle,
+        pclass=parcels.Particle,
         start=(30.0, 30.0),
         finish=(30.0, 50.0),
     )  # One particle in centre, one on periphery of Field.

docs/examples/example_stommel.py

@@ -127,7 +127,7 @@ def stommel_example(
         parcels.Variable("next_dt", dtype=np.float64, initial=dt.total_seconds()),
         parcels.Variable("age", dtype=np.float32, initial=0.0),
     ]
-    MyParticle = parcels.ScipyParticle.add_variables(extra_vars)
+    MyParticle = parcels.Particle.add_variables(extra_vars)
 
     if custom_partition_function:
         pset = parcels.ParticleSet.from_line(