[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

src/parcels/_core/particlefile.py

@@ -9,13 +9,13 @@
 import cftime
 import numpy as np
 import pyarrow as pa
-from parcels._typing import PathLike
 import pyarrow.parquet as pq
 
 import parcels
 from parcels._core.particle import ParticleClass
 from parcels._core.utils.time import timedelta_to_float
 from parcels._reprs import particlefile_repr
+from parcels._typing import PathLike
 
 if TYPE_CHECKING:
     from parcels._core.particle import Variable
@@ -69,14 +69,16 @@ def __init__(self, path: PathLike, outputdt):
         path = Path(path)
 
         if path.suffix != ".parquet":
-            raise ValueError(f"ParticleFile data is stored in Parquet files - file extension must be '.parquet'. Got {path.suffix=!r}.")
+            raise ValueError(
+                f"ParticleFile data is stored in Parquet files - file extension must be '.parquet'. Got {path.suffix=!r}."
+            )
 
         if outputdt <= 0:
             raise ValueError(f"outputdt must be positive/non-zero. Got {outputdt=!r}")
 
         self._outputdt = outputdt
 
-        self._path = path # TODO v4: Consider https://arrow.apache.org/docs/python/getstarted.html#working-with-large-data - though a significant question becomes how to partition, perhaps using a particle variable "partition"?
+        self._path = path  # TODO v4: Consider https://arrow.apache.org/docs/python/getstarted.html#working-with-large-data - though a significant question becomes how to partition, perhaps using a particle variable "partition"?
         self._writer: pq.ParquetWriter | None = None
         if path.exists():
             # TODO: Add logic for recovering/appending to existing parquet file
@@ -138,7 +140,7 @@ def write(self, pset: ParticleSet, time, indices=None):
             indices_to_write = _to_write_particles(particle_data, time)
         else:
             indices_to_write = indices
-        
+
         self._writer.write_table(
             pa.table({v.name: pa.array(particle_data[v.name][indices_to_write]) for v in vars_to_write}),
         )

src/parcels/_core/particleset.py

@@ -453,7 +453,7 @@ def execute(
 
         if output_file is not None:
             output_file.close()
-            
+
         if verbose_progress:
             pbar.close()
 

src/parcels/_reprs.py

@@ -7,7 +7,6 @@
 
 import numpy as np
 import xarray as xr
-from zarr.storage import DirectoryStore
 
 if TYPE_CHECKING:
     from parcels import Field, FieldSet, ParticleSet
@@ -178,6 +177,5 @@ def _format_list_items_multiline(items: list[str] | dict, level: int = 1, with_b
         return "\n".join([textwrap.indent(e, indentation_str) for e in entries])
 
 
-
 def is_builtin_object(obj):
     return obj.__class__.__module__ == "builtins"

tests/conftest.py

@@ -12,7 +12,7 @@ def tmp_parquet(tmp_path, request):
 def tmp_store():
     return MemoryStore()
 
+
 @pytest.fixture
 def tmp_parquet(tmp_path):
-    return tmp_path / 'tmp.parquet'
-
+    return tmp_path / "tmp.parquet"

tests/test_advection.py

@@ -1,10 +1,10 @@
 import numpy as np
+import pandas as pd
 import pytest
 import xarray as xr
 
 import parcels
 import parcels.tutorial
-import pandas as pd
 from parcels import (
     Field,
     FieldSet,

tests/test_fieldset.py

@@ -3,8 +3,8 @@
 import cf_xarray  # noqa: F401
 import cftime
 import numpy as np
-import pytest
 import pandas as pd
+import pytest
 import xarray as xr
 
 from parcels import Field, ParticleFile, ParticleSet, VectorField, XGrid, convert
@@ -96,7 +96,6 @@ def test_fieldset_gridset(fieldset):
     assert len(fieldset.gridset) == 2
 
 
-
 def test_fieldset_no_UV(tmp_parquet):
     grid = XGrid.from_dataset(ds, mesh="flat")
     fieldset = FieldSet([Field("P", ds["U_A_grid"], grid, interp_method=XLinear)])

tests/test_particlefile.py

@@ -2,13 +2,13 @@
 import tempfile
 from contextlib import nullcontext as does_not_raise
 from datetime import datetime, timedelta
-import pyarrow.parquet as pq
-import pandas as pd
+
 import numpy as np
+import pandas as pd
 import pyarrow as pa
+import pyarrow.parquet as pq
 import pytest
 import xarray as xr
-from zarr.storage import MemoryStore
 
 import parcels.tutorial
 from parcels import (
@@ -22,9 +22,9 @@
     VectorField,
     XGrid,
 )
-from parcels._core.particle import Particle, create_particle_data, get_default_particle
+from parcels._core.particle import Particle, get_default_particle
 from parcels._core.particlefile import _get_schema
-from parcels._core.utils.time import TimeInterval, timedelta_to_float
+from parcels._core.utils.time import timedelta_to_float
 from parcels._datasets.structured.generated import peninsula_dataset
 from parcels._datasets.structured.generic import datasets
 from parcels.convert import copernicusmarine_to_sgrid
@@ -343,7 +343,7 @@ def Update_lon(particles, fieldset):  # pragma: no cover
     pset.execute(Update_lon, runtime=np.timedelta64(11, "s"), dt=np.timedelta64(2, "s"), output_file=ofile)
 
     df = pd.read_parquet(tmp_parquet)
-    assert np.allclose(df['lon'].values, [0, 3, 6, 9])
+    assert np.allclose(df["lon"].values, [0, 3, 6, 9])
     pytest.skip("# TODO: Need to figure out how times work with parquet output (#2386)")
     assert np.allclose(timedelta_to_float(df.time.values - df.time.values[0, 0]), [0, 3, 6, 9])
 

tests/test_uxadvection.py

@@ -1,6 +1,6 @@
 import numpy as np
+import pandas as pd
 import pytest
-import xarray as xr
 
 import parcels
 from parcels._datasets.unstructured.generic import datasets as datasets_unstructured
@@ -9,8 +9,6 @@
     AdvectionRK2,
     AdvectionRK4,
 )
-import pandas as pd
-
 
 
 @pytest.mark.parametrize("integrator", [AdvectionEE, AdvectionRK2, AdvectionRK4])