Merge branch 'master' into croco_3D_velocities

.git-blame-ignore-revs

@@ -6,3 +6,6 @@ e99e0d170a7dc128031b82ea00cdf9e9a0164b03
 
 # Run black on examples
 cbf96c4e1f58fa6348695d7553900ba3f7c3383b
+
+# Run Ruff format on codebase
+19dd7eb1370063f252f94dd26bf313ff71484876

docs/conf.py

@@ -399,7 +399,7 @@ def linkcode_resolve(domain, info):
         master_doc,
         "parcels.tex",
         "Parcels Documentation",
-        "M. Lange, E. van Sebille",
+        "The Parcels developers",
         "manual",
     ),
 ]

parcels/application_kernels/advection.py

@@ -42,9 +42,9 @@ def AdvectionRK4_3D(particle, fieldset, time):
     lat3 = particle.lat + v3 * particle.dt
     dep3 = particle.depth + w3 * particle.dt
     (u4, v4, w4) = fieldset.UVW[time + particle.dt, dep3, lat3, lon3, particle]
-    particle_dlon += (u1 + 2 * u2 + 2 * u3 + u4) / 6.0 * particle.dt  # noqa
-    particle_dlat += (v1 + 2 * v2 + 2 * v3 + v4) / 6.0 * particle.dt  # noqa
-    particle_ddepth += (w1 + 2 * w2 + 2 * w3 + w4) / 6.0 * particle.dt  # noqa
+    particle_dlon += (u1 + 2 * u2 + 2 * u3 + u4) / 6 * particle.dt  # noqa
+    particle_dlat += (v1 + 2 * v2 + 2 * v3 + v4) / 6 * particle.dt  # noqa
+    particle_ddepth += (w1 + 2 * w2 + 2 * w3 + w4) / 6 * particle.dt  # noqa
 
 
 def AdvectionRK4_3D_CROCO(particle, fieldset, time):
@@ -81,15 +81,15 @@ def AdvectionRK4_3D_CROCO(particle, fieldset, time):
     sig_dep4 = sig_dep + w4 * particle.dt
     dep4 = sig_dep4 * fieldset.H[time, 0, lat4, lon4]
 
-    particle_dlon += (u1 + 2 * u2 + 2 * u3 + u4) / 6.0 * particle.dt  # noqa
-    particle_dlat += (v1 + 2 * v2 + 2 * v3 + v4) / 6.0 * particle.dt  # noqa
+    particle_dlon += (u1 + 2 * u2 + 2 * u3 + u4) / 6 * particle.dt  # noqa
+    particle_dlat += (v1 + 2 * v2 + 2 * v3 + v4) / 6 * particle.dt  # noqa
     particle_ddepth += (  # noqa
         (dep1 - particle.depth) * 2
         + 2 * (dep2 - particle.depth) * 2
         + 2 * (dep3 - particle.depth)
         + dep4
         - particle.depth
-    ) / 6.0
+    ) / 6
 
 
 def AdvectionEE(particle, fieldset, time):

parcels/compilation/codegenerator.py

@@ -629,7 +629,7 @@ def visit_Assign(self, node):
             self.array_vars += [node.targets[0].id]
         elif isinstance(node.value, ParticleXiYiZiTiAttributeNode):
             raise RuntimeError(
-                f"Add index of the grid when using particle.{node.value.attr} " f"(e.g. particle.{node.value.attr}[0])."
+                f"Add index of the grid when using particle.{node.value.attr} (e.g. particle.{node.value.attr}[0])."
             )
         else:
             node.ccode = c.Assign(node.targets[0].ccode, node.value.ccode)

parcels/field.py

@@ -1565,7 +1565,7 @@ def write(self, filename, varname=None):
         if varname is None:
             varname = self.name
         # Derive name of 'depth' variable for NEMO convention
-        vname_depth = "depth%s" % self.name.lower()
+        vname_depth = f"depth{self.name.lower()}"
 
         # Create DataArray objects for file I/O
         if self.grid.gtype == GridType.RectilinearZGrid:

parcels/interaction/interactionkernel.py

@@ -80,7 +80,7 @@ def __init__(
 
         if self._ptype.uses_jit:
             raise NotImplementedError(
-                "JIT mode is not supported for" " InteractionKernels. Please run your" " simulation in SciPy mode."
+                "JIT mode is not supported for InteractionKernels. Please run your simulation in SciPy mode."
             )
 
         for func in self._pyfunc:
@@ -166,7 +166,7 @@ def cleanup_unload_lib(lib):
 
     def execute_jit(self, pset, endtime, dt):
         raise NotImplementedError(
-            "JIT mode is not supported for" " InteractionKernels. Please run your" " simulation in SciPy mode."
+            "JIT mode is not supported for InteractionKernels. Please run your simulation in SciPy mode."
         )
 
     def execute_python(self, pset, endtime, dt):

parcels/particledata.py

@@ -68,9 +68,9 @@ def __init__(self, pclass, lon, lat, depth, time, lonlatdepth_dtype, pid_orig, n
         assert (
             depth is not None
         ), "particle's initial depth is None - incompatible with the ParticleData class. Invalid state."
-        assert lon.size == lat.size and lon.size == depth.size, "lon, lat, depth don" "t all have the same lenghts."
+        assert lon.size == lat.size and lon.size == depth.size, "lon, lat, depth don't all have the same lenghts."
 
-        assert lon.size == time.size, "time and positions (lon, lat, depth) don" "t have the same lengths."
+        assert lon.size == time.size, "time and positions (lon, lat, depth) don't have the same lengths."
 
         # If a partitioning function for MPI runs has been passed into the
         # particle creation with the "partition_function" kwarg, retrieve it here.

parcels/particlefile.py

@@ -212,9 +212,10 @@ def write(self, pset, time, indices=None):
             logger.warning("ParticleSet is empty on writing as array at time %g" % time)
             return
 
-        indices_to_write = (
-            pset.particledata._to_write_particles(pset.particledata._data, time) if indices is None else indices
-        )
+        if indices is None:
+            indices_to_write = pset.particledata._to_write_particles(pset.particledata._data, time)
+        else:
+            indices_to_write = indices
 
         if len(indices_to_write) > 0:
             pids = pset.particledata.getvardata("id", indices_to_write)

parcels/particleset.py

@@ -166,7 +166,7 @@ def ArrayClass_init(self, *args, **kwargs):
             depth = np.ones(lon.size) * mindepth
         else:
             depth = convert_to_flat_array(depth)
-        assert lon.size == lat.size and lon.size == depth.size, "lon, lat, depth don" "t all have the same lenghts"
+        assert lon.size == lat.size and lon.size == depth.size, "lon, lat, depth don't all have the same lenghts"
 
         time = convert_to_flat_array(time)
         time = np.repeat(time, lon.size) if time.size == 1 else time
@@ -176,7 +176,7 @@ def ArrayClass_init(self, *args, **kwargs):
         if time.size > 0 and isinstance(time[0], np.timedelta64) and not self.time_origin:
             raise NotImplementedError("If fieldset.time_origin is not a date, time of a particle must be a double")
         time = np.array([self.time_origin.reltime(t) if _convert_to_reltime(t) else t for t in time])
-        assert lon.size == time.size, "time and positions (lon, lat, depth) don" "t have the same lengths."
+        assert lon.size == time.size, "time and positions (lon, lat, depth) do not have the same lengths."
 
         if lonlatdepth_dtype is None:
             lonlatdepth_dtype = self.lonlatdepth_dtype_from_field_interp_method(fieldset.U)
@@ -244,7 +244,7 @@ def ArrayClass_init(self, *args, **kwargs):
                 else:
                     interaction_class = KDTreeFlatNeighborSearch
             else:
-                assert False, "Interaction is only possible on 'flat' and " "'spherical' meshes"
+                assert False, "Interaction is only possible on 'flat' and 'spherical' meshes"
             try:
                 if len(interaction_distance) == 2:
                     inter_dist_vert, inter_dist_horiz = interaction_distance

parcels/tools/converters.py

@@ -281,10 +281,8 @@ def convert_xarray_time_units(ds, time):
         da2 = xr.decode_cf(da2)
     except ValueError:
         raise RuntimeError(
-            "Xarray could not convert the calendar. If you"
-            "re using from_netcdf, "
+            "Xarray could not convert the calendar. If you're using from_netcdf, "
             "try using the timestamps keyword in the construction of your Field. "
-            "See also the tutorial at https://docs.oceanparcels.org/en/latest/"
-            "examples/tutorial_timestamps.html"
+            "See also the tutorial at https://docs.oceanparcels.org/en/latest/examples/tutorial_timestamps.html"
         )
     ds[time] = da2[time]

parcels/tools/exampledata_utils.py

@@ -133,7 +133,7 @@ def download_example_dataset(dataset: str, data_home=None):
     # Dev note: `dataset` is assumed to be a folder name with netcdf files
     if dataset not in example_data_files:
         raise ValueError(
-            f"Dataset {dataset!r} not found. Available datasets are: " ", ".join(example_data_files.keys())
+            f"Dataset {dataset!r} not found. Available datasets are: " + ", ".join(example_data_files.keys())
         )
 
     cache_folder = get_data_home(data_home)

pyproject.toml

@@ -71,6 +71,7 @@ select = [
     "ICN", # import conventions
     "G", # logging-format
     "RUF", # ruff
+    "ISC001", # single-line-implicit-string-concatenation
 ]
 
 ignore = [

tests/test_kernel_language.py

@@ -27,7 +27,8 @@
 
 
 def expr_kernel(name, pset, expr):
-    pycode = f"def {name}(particle, fieldset, time):\n" f"    particle.p = {expr}"
+    pycode = (f"def {name}(particle, fieldset, time):\n"
+              f"    particle.p = {expr}")  # fmt: skip
     return Kernel(
         pset.fieldset, pset.particledata.ptype, pyfunc=None, funccode=pycode, funcname=name, funcvars=["particle"]
     )