Merge branch 'master' into vectorial_summing_zarr_approach

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+ignore =
+    # missing whitespace around arithmetic operator
+    E226,
+    # do not use bare except, specify exception instead
+    E722,
+    # line break before binary operator
+    W503,
+    # line too long (82 > 79 characters)
+    E501,
+    # ‘from module import *’ used; unable to detect undefined names
+    F403,

.github/actions/install-parcels/action.yml

@@ -27,7 +27,7 @@ runs:
         cache-environment: true
         cache-downloads: true
     - name: Install parcels
-      run: python setup.py install
+      run: pip install .
       shell: bash -el {0}
     - name: Set env variables for macos
       run: |

.gitignore

@@ -18,6 +18,7 @@ out-*
 **/*.zarr/*
 
 .idea/*
+.env
 Profile.prof
 **/.ipynb_checkpoints/*
 .cache/*

docs/conf.py

@@ -1,4 +1,4 @@
-#
+"""Sphinx configuration file for Parcels documentation."""
 # parcels documentation build configuration file, created by
 # sphinx-quickstart on Tue Oct 20 09:58:20 2015.
 #
@@ -209,6 +209,7 @@
 
 
 def make_filename_safe(filename: str, safe_char: str = '_') -> str:
+    """Make a filename safe for saving to disk."""
     # Replace any characters that are not allowed in a filename with the safe character
     safe_filename = re.sub(r'[\\/:*?"<>|]', safe_char, filename)
     return safe_filename
@@ -356,9 +357,9 @@ def linkcode_resolve(domain, info):
     'examples/tutorial_timestamps': '_static/calendar-icon.jpg',
     'examples/tutorial_jit_vs_scipy': '_static/clock-icon.png',
     'examples/documentation_homepage_animation': '_images/homepage.gif',
-    'examples/tutorial_Agulhasparticles': '_images/globcurrent_fullyseeded.gif',
     'examples/tutorial_interaction': '_static/pulled_particles_twoatractors_line.gif',
     'examples/documentation_LargeRunsOutput': '_static/harddrive.png',
+    'examples/tutorial_unitconverters': '_static/globe-icon.jpg',
     'examples/documentation_geospatial': '_images/tutorial_geospatial_google_earth.png'
 }
 # -- Options for LaTeX output ---------------------------------------------

docs/documentation.rst

@@ -58,7 +58,6 @@ Parcels has several documentation and tutorial Jupyter notebooks which go throug
    examples/documentation_unstuck_Agrid.ipynb
    examples/documentation_LargeRunsOutput.ipynb
    examples/documentation_geospatial.ipynb
-   examples/tutorial_plotting.ipynb
    examples/documentation_advanced_zarr.ipynb
 
 
@@ -68,4 +67,3 @@ Parcels has several documentation and tutorial Jupyter notebooks which go throug
 
    examples/tutorial_Argofloats.ipynb
    examples/documentation_homepage_animation.ipynb
-   examples/tutorial_Agulhasparticles.ipynb

docs/examples/documentation_indexing.ipynb

@@ -87,7 +87,7 @@
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
-      "\u001b[1;32m/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb Cell 5\u001b[0m in \u001b[0;36m<cell line: 29>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=6'>7</a>\u001b[0m variables \u001b[39m=\u001b[39m {\u001b[39m\"\u001b[39m\u001b[39mU\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39muo\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39mV\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mvo\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39mW\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mwo\u001b[39m\u001b[39m\"\u001b[39m}\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=7'>8</a>\u001b[0m dimensions \u001b[39m=\u001b[39m {\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=8'>9</a>\u001b[0m     \u001b[39m\"\u001b[39m\u001b[39mU\u001b[39m\u001b[39m\"\u001b[39m: {\n\u001b[1;32m     <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=9'>10</a>\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mlon\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mnav_lon\u001b[39m\u001b[39m\"\u001b[39m,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=25'>26</a>\u001b[0m     },\n\u001b[1;32m     <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=26'>27</a>\u001b[0m }\n\u001b[0;32m---> <a href='vscode-notebook-cell:/Users/erik/Codes/ParcelsCode/docs/examples/documentation_indexing.ipynb#W4sZmlsZQ%3D%3D?line=28'>29</a>\u001b[0m fieldset \u001b[39m=\u001b[39m FieldSet\u001b[39m.\u001b[39;49mfrom_nemo(filenames, variables, dimensions)\n",
+      "Cell \u001b[0;32mIn[2], line 29\u001b[0m\n\u001b[1;32m      7\u001b[0m variables \u001b[39m=\u001b[39m {\u001b[39m\"\u001b[39m\u001b[39mU\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39muo\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39mV\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mvo\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39mW\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mwo\u001b[39m\u001b[39m\"\u001b[39m}\n\u001b[1;32m      8\u001b[0m dimensions \u001b[39m=\u001b[39m {\n\u001b[1;32m      9\u001b[0m     \u001b[39m\"\u001b[39m\u001b[39mU\u001b[39m\u001b[39m\"\u001b[39m: {\n\u001b[1;32m     10\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mlon\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mnav_lon\u001b[39m\u001b[39m\"\u001b[39m,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     26\u001b[0m     },\n\u001b[1;32m     27\u001b[0m }\n\u001b[0;32m---> 29\u001b[0m fieldset \u001b[39m=\u001b[39m FieldSet\u001b[39m.\u001b[39;49mfrom_nemo(filenames, variables, dimensions)\n",
       "File \u001b[0;32m~/Codes/ParcelsCode/parcels/fieldset.py:561\u001b[0m, in \u001b[0;36mFieldSet.from_nemo\u001b[0;34m(cls, filenames, variables, dimensions, indices, mesh, allow_time_extrapolation, time_periodic, tracer_interp_method, chunksize, **kwargs)\u001b[0m\n\u001b[1;32m    559\u001b[0m \u001b[39mif\u001b[39;00m kwargs\u001b[39m.\u001b[39mpop(\u001b[39m'\u001b[39m\u001b[39mgridindexingtype\u001b[39m\u001b[39m'\u001b[39m, \u001b[39m'\u001b[39m\u001b[39mnemo\u001b[39m\u001b[39m'\u001b[39m) \u001b[39m!=\u001b[39m \u001b[39m'\u001b[39m\u001b[39mnemo\u001b[39m\u001b[39m'\u001b[39m:\n\u001b[1;32m    560\u001b[0m     \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mgridindexingtype must be \u001b[39m\u001b[39m'\u001b[39m\u001b[39mnemo\u001b[39m\u001b[39m'\u001b[39m\u001b[39m in FieldSet.from_nemo(). Use FieldSet.from_c_grid_dataset otherwise\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[0;32m--> 561\u001b[0m fieldset \u001b[39m=\u001b[39m \u001b[39mcls\u001b[39;49m\u001b[39m.\u001b[39;49mfrom_c_grid_dataset(filenames, variables, dimensions, mesh\u001b[39m=\u001b[39;49mmesh, indices\u001b[39m=\u001b[39;49mindices, time_periodic\u001b[39m=\u001b[39;49mtime_periodic,\n\u001b[1;32m    562\u001b[0m                                    allow_time_extrapolation\u001b[39m=\u001b[39;49mallow_time_extrapolation, tracer_interp_method\u001b[39m=\u001b[39;49mtracer_interp_method,\n\u001b[1;32m    563\u001b[0m                                    chunksize\u001b[39m=\u001b[39;49mchunksize, gridindexingtype\u001b[39m=\u001b[39;49m\u001b[39m'\u001b[39;49m\u001b[39mnemo\u001b[39;49m\u001b[39m'\u001b[39;49m, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mkwargs)\n\u001b[1;32m    564\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mhasattr\u001b[39m(fieldset, \u001b[39m'\u001b[39m\u001b[39mW\u001b[39m\u001b[39m'\u001b[39m):\n\u001b[1;32m    565\u001b[0m     fieldset\u001b[39m.\u001b[39mW\u001b[39m.\u001b[39mset_scaling_factor(\u001b[39m-\u001b[39m\u001b[39m1.\u001b[39m)\n",
       "File \u001b[0;32m~/Codes/ParcelsCode/parcels/fieldset.py:672\u001b[0m, in \u001b[0;36mFieldSet.from_c_grid_dataset\u001b[0;34m(cls, filenames, variables, dimensions, indices, mesh, allow_time_extrapolation, time_periodic, tracer_interp_method, gridindexingtype, chunksize, **kwargs)\u001b[0m\n\u001b[1;32m    600\u001b[0m \u001b[39m\"\"\"Initialises FieldSet object from NetCDF files of Curvilinear NEMO fields.\u001b[39;00m\n\u001b[1;32m    601\u001b[0m \n\u001b[1;32m    602\u001b[0m \u001b[39mSee `here <../examples/documentation_indexing.ipynb>`__\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    669\u001b[0m \u001b[39m    Keyword arguments passed to the :func:`Fieldset.from_netcdf` constructor.\u001b[39;00m\n\u001b[1;32m    670\u001b[0m \u001b[39m\"\"\"\u001b[39;00m\n\u001b[1;32m    671\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39m'\u001b[39m\u001b[39mU\u001b[39m\u001b[39m'\u001b[39m \u001b[39min\u001b[39;00m dimensions \u001b[39mand\u001b[39;00m \u001b[39m'\u001b[39m\u001b[39mV\u001b[39m\u001b[39m'\u001b[39m \u001b[39min\u001b[39;00m dimensions \u001b[39mand\u001b[39;00m dimensions[\u001b[39m'\u001b[39m\u001b[39mU\u001b[39m\u001b[39m'\u001b[39m] \u001b[39m!=\u001b[39m dimensions[\u001b[39m'\u001b[39m\u001b[39mV\u001b[39m\u001b[39m'\u001b[39m]:\n\u001b[0;32m--> 672\u001b[0m     \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mOn a C-grid, the dimensions of velocities should be the corners (f-points) of the cells, so the same for U and V. \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    673\u001b[0m                      \u001b[39m\"\u001b[39m\u001b[39mSee also ../examples/documentation_indexing.ipynb\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m    674\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39m'\u001b[39m\u001b[39mU\u001b[39m\u001b[39m'\u001b[39m \u001b[39min\u001b[39;00m dimensions \u001b[39mand\u001b[39;00m \u001b[39m'\u001b[39m\u001b[39mW\u001b[39m\u001b[39m'\u001b[39m \u001b[39min\u001b[39;00m dimensions \u001b[39mand\u001b[39;00m dimensions[\u001b[39m'\u001b[39m\u001b[39mU\u001b[39m\u001b[39m'\u001b[39m] \u001b[39m!=\u001b[39m dimensions[\u001b[39m'\u001b[39m\u001b[39mW\u001b[39m\u001b[39m'\u001b[39m]:\n\u001b[1;32m    675\u001b[0m     \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mOn a C-grid, the dimensions of velocities should be the corners (f-points) of the cells, so the same for U, V and W. \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    676\u001b[0m                      \u001b[39m\"\u001b[39m\u001b[39mSee also ../examples/documentation_indexing.ipynb\u001b[39m\u001b[39m\"\u001b[39m)\n",
       "\u001b[0;31mValueError\u001b[0m: On a C-grid, the dimensions of velocities should be the corners (f-points) of the cells, so the same for U and V. See also ../examples/documentation_indexing.ipynb"
@@ -216,7 +216,6 @@
     }
    ],
    "source": [
-    "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
     "from mpl_toolkits.mplot3d import Axes3D  # noqa\n",
     "\n",
@@ -293,7 +292,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.10.9"
   }
  },
  "nbformat": 4,

docs/examples/example_decaying_moving_eddy.py

@@ -58,7 +58,7 @@ def decaying_moving_example(fieldset, outfile, mode='scipy', method=AdvectionRK4
     runtime = delta(days=2)
     outputdt = delta(hours=1)
 
-    pset.execute(method, runtime=runtime, dt=dt, moviedt=None,
+    pset.execute(method, runtime=runtime, dt=dt,
                  output_file=pset.ParticleFile(name=outfile, outputdt=outputdt))
 
     return pset

docs/examples/example_moving_eddies.py

@@ -133,8 +133,7 @@ def moving_eddies_example(fieldset, outfile, npart=2, mode='jit', verbose=False,
     runtime = delta(days=7)
     print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
     pset.execute(method, runtime=runtime, dt=delta(hours=1),
-                 output_file=pset.ParticleFile(name=outfile, outputdt=delta(hours=1)),
-                 moviedt=None)
+                 output_file=pset.ParticleFile(name=outfile, outputdt=delta(hours=1)))
 
     if verbose:
         print(f"Final particle positions:\n{pset}")

docs/examples/example_nemo_curvilinear.py

@@ -1,3 +1,4 @@
+"""Example script that runs a set of particles in a NEMO curvilinear grid."""
 from argparse import ArgumentParser
 from datetime import timedelta as delta
 from glob import glob
@@ -21,7 +22,7 @@
 
 
 def run_nemo_curvilinear(mode, outfile, advtype='RK4'):
-    """Function that shows how to read in curvilinear grids, in this case from NEMO."""
+    """Run parcels on the NEMO curvilinear grid."""
     data_folder = download_example_dataset('NemoCurvilinear_data')
 
     filenames = {'U': {'lon': f'{data_folder}/mesh_mask.nc4',
@@ -58,41 +59,21 @@ def periodicBC(particle, fieldSet, time):
     assert np.allclose(pset.lat - latp, 0, atol=2e-2)
 
 
-def make_plot(trajfile):
-    import cartopy
-    import matplotlib.pyplot as plt
-    import xarray as xr
-
-    class ParticleData:
-        def __init__(self):
-            self.id = []
-
-    def load_particles_file(fname, varnames):
-        T = ParticleData()
-        ds = xr.open_zarr(fname)
-        T.id = ds['trajectory'][:]
-        for v in varnames:
-            setattr(T, v, ds[v][:])
-        return T
-
-    T = load_particles_file(trajfile, ['lon', 'lat', 'time'])
-    plt.axes(projection=cartopy.crs.PlateCarree())
-    plt.scatter(T.lon, T.lat, c=T.time, s=10)
-    plt.show()
-
-
 @pytest.mark.parametrize('mode', ['jit'])  # Only testing jit as scipy is very slow
 def test_nemo_curvilinear(mode, tmpdir):
+    """Test the NEMO curvilinear example."""
     outfile = tmpdir.join('nemo_particles')
     run_nemo_curvilinear(mode, outfile)
 
 
 def test_nemo_curvilinear_AA(tmpdir):
+    """Test the NEMO curvilinear example with analytical advection."""
     outfile = tmpdir.join('nemo_particlesAA')
     run_nemo_curvilinear('scipy', outfile, 'AA')
 
 
 def test_nemo_3D_samegrid():
+    """Test that the same grid is used for U and V in 3D NEMO fields."""
     data_folder = download_example_dataset('NemoNorthSeaORCA025-N006_data')
     ufiles = sorted(glob(f'{data_folder}/ORCA*U.nc'))
     vfiles = sorted(glob(f'{data_folder}/ORCA*V.nc'))
@@ -116,6 +97,7 @@ def test_nemo_3D_samegrid():
 
 
 def main(args=None):
+    """Run the example with given arguments."""
     p = ArgumentParser(description="""Chose the mode using mode option""")
     p.add_argument('mode', choices=('scipy', 'jit'), nargs='?', default='jit',
                    help='Execution mode for performing computation')
@@ -124,7 +106,6 @@ def main(args=None):
     outfile = "nemo_particles"
 
     run_nemo_curvilinear(args.mode, outfile)
-    make_plot(outfile+'.zarr')
 
 
 if __name__ == "__main__":

docs/examples/example_radial_rotation.py

@@ -60,7 +60,7 @@ def rotation_example(fieldset, outfile, mode='jit', method=AdvectionRK4):
     dt = delta(minutes=5)
     outputdt = delta(hours=1)
 
-    pset.execute(method, runtime=runtime, dt=dt, moviedt=None,
+    pset.execute(method, runtime=runtime, dt=dt,
                  output_file=pset.ParticleFile(name=outfile, outputdt=outputdt))
 
     return pset

docs/examples/example_stommel.py

@@ -121,7 +121,7 @@ class MyParticle(ParticleClass):
     timer.psetinit.stop()
     timer.psetrun = timer.Timer('Pset_run', parent=timer.pset)
     pset.execute(method + pset.Kernel(UpdateP) + pset.Kernel(AgeP), runtime=runtime, dt=dt,
-                 moviedt=None, output_file=pset.ParticleFile(name=outfile, outputdt=outputdt))
+                 output_file=pset.ParticleFile(name=outfile, outputdt=outputdt))
 
     if verbose:
         print(f"Final particle positions:\n{pset}")