Merge pull request #1776 from OceanParcels/pre-commit-ci-update-config

VeckoTheGecko · web-flow · commit 5a42675521d7 · 2024-11-29T16:43:40.000+08:00
[pre-commit.ci] pre-commit autoupdate
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ repos:
         types: [text]
         files: \.(json|ipynb)$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.8.0
     hooks:
       - id: ruff
         name: ruff lint (.py)
diff --git a/docs/examples/example_dask_chunk_OCMs.py b/docs/examples/example_dask_chunk_OCMs.py
@@ -247,7 +247,7 @@ def test_pop(mode, chunk_mode):
     filenames = str(data_folder / "t.x1_SAMOC_flux.1690*.nc")
     variables = {"U": "UVEL", "V": "VVEL", "W": "WVEL"}
     timestamps = np.expand_dims(
-        np.array([np.datetime64("2000-%.2d-01" % m) for m in range(1, 7)]), axis=1
+        np.array([np.datetime64(f"2000-{m:02d}-01") for m in range(1, 7)]), axis=1
     )
     dimensions = {"lon": "ULON", "lat": "ULAT", "depth": "w_dep"}
     chs = False
diff --git a/docs/examples/example_moving_eddies.py b/docs/examples/example_moving_eddies.py
@@ -146,7 +146,7 @@ def moving_eddies_example(
 
     # Execute for 1 week, with 1 hour timesteps and hourly output
     runtime = timedelta(days=7)
-    print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
+    print(f"MovingEddies: Advecting {npart} particles for {runtime}")
     pset.execute(
         method,
         runtime=runtime,
@@ -177,7 +177,7 @@ def test_moving_eddies_fwdbwd(mode, mesh, tmpdir, npart=2):
     runtime = timedelta(days=1)
     dt = timedelta(minutes=5)
     outputdt = timedelta(hours=1)
-    print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
+    print(f"MovingEddies: Advecting {npart} particles for {runtime}")
     outfile = tmpdir.join("EddyParticlefwd")
     pset.execute(
         method,
diff --git a/docs/examples/example_peninsula.py b/docs/examples/example_peninsula.py
@@ -168,7 +168,7 @@ def peninsula_example(
     out = (
         pset.ParticleFile(name=outfile, outputdt=timedelta(hours=1)) if output else None
     )
-    print("Peninsula: Advecting %d particles for %s" % (npart, str(time)))
+    print(f"Peninsula: Advecting {npart} particles for {time}")
     pset.execute(k_adv + k_p, runtime=time, dt=dt, output_file=out)
 
     if verbose:
diff --git a/docs/examples/example_stommel.py b/docs/examples/example_stommel.py
@@ -160,7 +160,7 @@ def stommel_example(
 
     maxage = runtime.total_seconds() if maxage is None else maxage
     fieldset.add_constant("maxage", maxage)
-    print("Stommel: Advecting %d particles for %s" % (npart, runtime))
+    print(f"Stommel: Advecting {npart} particles for {runtime}")
     parcels.timer.psetinit.stop()
     parcels.timer.psetrun = parcels.timer.Timer("Pset_run", parent=parcels.timer.pset)
     pset.execute(
diff --git a/parcels/application_kernels/EOSseawaterproperties.py b/parcels/application_kernels/EOSseawaterproperties.py
@@ -2,7 +2,7 @@
 
 import math
 
-__all__ = ["PressureFromLatDepth", "AdiabticTemperatureGradient", "PtempFromTemp", "TempFromPtemp", "UNESCODensity"]
+__all__ = ["AdiabticTemperatureGradient", "PressureFromLatDepth", "PtempFromTemp", "TempFromPtemp", "UNESCODensity"]
 
 
 def PressureFromLatDepth(particle, fieldset, time):
diff --git a/parcels/application_kernels/advection.py b/parcels/application_kernels/advection.py
@@ -5,12 +5,12 @@
 from parcels.tools.statuscodes import StatusCode
 
 __all__ = [
-    "AdvectionRK4",
+    "AdvectionAnalytical",
     "AdvectionEE",
-    "AdvectionRK45",
+    "AdvectionRK4",
     "AdvectionRK4_3D",
-    "AdvectionAnalytical",
     "AdvectionRK4_3D_CROCO",
+    "AdvectionRK45",
 ]
 
 
diff --git a/parcels/application_kernels/advectiondiffusion.py b/parcels/application_kernels/advectiondiffusion.py
@@ -7,7 +7,7 @@
 
 import parcels
 
-__all__ = ["DiffusionUniformKh", "AdvectionDiffusionM1", "AdvectionDiffusionEM"]
+__all__ = ["AdvectionDiffusionEM", "AdvectionDiffusionM1", "DiffusionUniformKh"]
 
 
 def AdvectionDiffusionM1(particle, fieldset, time):
diff --git a/parcels/application_kernels/interaction.py b/parcels/application_kernels/interaction.py
@@ -4,7 +4,7 @@
 
 from parcels.tools.statuscodes import StatusCode
 
-__all__ = ["AsymmetricAttraction", "NearestNeighborWithinRange", "MergeWithNearestNeighbor"]
+__all__ = ["AsymmetricAttraction", "MergeWithNearestNeighbor", "NearestNeighborWithinRange"]
 
 
 def NearestNeighborWithinRange(particle, fieldset, time, neighbors, mutator):
diff --git a/parcels/compilation/codegenerator.py b/parcels/compilation/codegenerator.py
@@ -226,7 +226,7 @@ def __init__(self, fieldset=None, ptype=JITParticle):
 
     def get_tmp(self):
         """Create a new temporary variable name."""
-        tmp = "parcels_tmpvar%d" % self._tmp_counter
+        tmp = f"parcels_tmpvar{self._tmp_counter:d}"
         self._tmp_counter += 1
         self.tmp_vars += [tmp]
         return tmp
diff --git a/parcels/field.py b/parcels/field.py
@@ -50,7 +50,7 @@
 
     from parcels.fieldset import FieldSet
 
-__all__ = ["Field", "VectorField", "NestedField"]
+__all__ = ["Field", "NestedField", "VectorField"]
 
 
 def _isParticle(key):
@@ -1242,7 +1242,7 @@ def _search_indices_curvilinear(self, x, y, z, ti=-1, time=-1, particle=None, se
             (xi, yi) = self._reconnect_bnd_indices(xi, yi, grid.xdim, grid.ydim, grid.mesh)
             it += 1
             if it > maxIterSearch:
-                print("Correct cell not found after %d iterations" % maxIterSearch)
+                print(f"Correct cell not found after {maxIterSearch} iterations")
                 raise FieldOutOfBoundError(x, y, 0, field=self)
         xsi = max(0.0, xsi)
         eta = max(0.0, eta)
@@ -1630,10 +1630,8 @@ def _chunk_data(self):
         g = self.grid
         if isinstance(self.data, da.core.Array):
             for block_id in range(len(self.grid._load_chunk)):
-                if (
-                    g._load_chunk[block_id] == g._chunk_loading_requested
-                    or g._load_chunk[block_id] in g._chunk_loaded
-                    and self._data_chunks[block_id] is None
+                if g._load_chunk[block_id] == g._chunk_loading_requested or (
+                    g._load_chunk[block_id] in g._chunk_loaded and self._data_chunks[block_id] is None
                 ):
                     block = self._get_block(block_id)
                     self._data_chunks[block_id] = np.array(
@@ -2534,13 +2532,13 @@ def __init__(self, name: str, F, V=None, W=None):
                 assert isinstance(Fi, Field) and isinstance(
                     Vi, Field
                 ), "F, and V components of a NestedField must be Field"
-                self.append(VectorField(name + "_%d" % i, Fi, Vi))
+                self.append(VectorField(f"{name}_{i}", Fi, Vi))
         else:
             for i, Fi, Vi, Wi in zip(range(len(F)), F, V, W, strict=True):
                 assert (
                     isinstance(Fi, Field) and isinstance(Vi, Field) and isinstance(Wi, Field)
                 ), "F, V and W components of a NestedField must be Field"
-                self.append(VectorField(name + "_%d" % i, Fi, Vi, Wi))
+                self.append(VectorField(f"{name}_{i}", Fi, Vi, Wi))
         self.name = name
 
     def __getitem__(self, key):
diff --git a/parcels/grid.py b/parcels/grid.py
@@ -12,14 +12,14 @@
 from parcels.tools.warnings import FieldSetWarning
 
 __all__ = [
-    "GridType",
-    "GridCode",
-    "RectilinearZGrid",
-    "RectilinearSGrid",
-    "CurvilinearZGrid",
-    "CurvilinearSGrid",
     "CGrid",
+    "CurvilinearSGrid",
+    "CurvilinearZGrid",
     "Grid",
+    "GridCode",
+    "GridType",
+    "RectilinearSGrid",
+    "RectilinearZGrid",
 ]
 
 
diff --git a/parcels/interaction/neighborsearch/__init__.py b/parcels/interaction/neighborsearch/__init__.py
@@ -11,9 +11,9 @@
 )
 
 __all__ = [
-    "HashFlatNeighborSearch",
-    "HashSphericalNeighborSearch",
     "BruteFlatNeighborSearch",
     "BruteSphericalNeighborSearch",
+    "HashFlatNeighborSearch",
+    "HashSphericalNeighborSearch",
     "KDTreeFlatNeighborSearch",
 ]
diff --git a/parcels/kernel.py b/parcels/kernel.py
@@ -42,7 +42,7 @@
 )
 from parcels.tools.warnings import KernelWarning
 
-__all__ = ["Kernel", "BaseKernel"]
+__all__ = ["BaseKernel", "Kernel"]
 
 
 class BaseKernel(abc.ABC):
@@ -418,7 +418,7 @@ def get_kernel_compile_files(self):
             dyn_dir = mpi_comm.bcast(dyn_dir, root=0)
             basename = cache_name if mpi_rank == 0 else None
             basename = mpi_comm.bcast(basename, root=0)
-            basename = basename + "_%d" % mpi_rank
+            basename = f"{basename}_{mpi_rank}"
         else:
             cache_name = (
                 self._cache_key
diff --git a/parcels/particle.py b/parcels/particle.py
@@ -6,7 +6,7 @@
 
 from parcels.tools.statuscodes import StatusCode
 
-__all__ = ["ScipyParticle", "JITParticle", "Variable", "ScipyInteractionParticle"]
+__all__ = ["JITParticle", "ScipyInteractionParticle", "ScipyParticle", "Variable"]
 
 indicators_64bit = [np.float64, np.uint64, np.int64, c_void_p]
 
@@ -201,7 +201,7 @@ def __del__(self):
 
     def __repr__(self):
         time_string = "not_yet_set" if self.time is None or np.isnan(self.time) else f"{self.time:f}"
-        p_string = "P[%d](lon=%f, lat=%f, depth=%f, " % (self.id, self.lon, self.lat, self.depth)
+        p_string = f"P[{self.id}](lon={self.lon:f}, lat={self.lat:f}, depth={self.depth:f}, "
         for var in vars(type(self)):
             if var in ["lon_nextloop", "lat_nextloop", "depth_nextloop", "time_nextloop"]:
                 continue
diff --git a/parcels/particledata.py b/parcels/particledata.py
@@ -460,7 +460,7 @@ def getPType(self):
 
     def __repr__(self):
         time_string = "not_yet_set" if self.time is None or np.isnan(self.time) else f"{self.time:f}"
-        p_string = "P[%d](lon=%f, lat=%f, depth=%f, " % (self.id, self.lon, self.lat, self.depth)
+        p_string = f"P[{self.id}](lon={self.lon:f}, lat={self.lat:f}, depth={self.depth:f}, "
         for var in self._pcoll.ptype.variables:
             if var.name in [
                 "lon_nextloop",
diff --git a/parcels/particleset.py b/parcels/particleset.py
@@ -1193,7 +1193,7 @@ def execute(
                             raise RuntimeError(
                                 "Field writing during execution only works for Fields with one snapshot in time"
                             )
-                        fldfilename = str(output_file.fname).replace(".zarr", "_%.4d" % fld.to_write)
+                        fldfilename = str(output_file.fname).replace(".zarr", f"_{fld.to_write:04d}")
                         fld.write(fldfilename)
                         fld.to_write += 1
 
diff --git a/parcels/rng.py b/parcels/rng.py
@@ -10,7 +10,7 @@
 from parcels.tools import get_cache_dir, get_package_dir
 from parcels.tools.loggers import logger
 
-__all__ = ["seed", "random", "uniform", "randint", "normalvariate", "expovariate", "vonmisesvariate"]
+__all__ = ["expovariate", "normalvariate", "randint", "random", "seed", "uniform", "vonmisesvariate"]
 
 
 class RandomC:
diff --git a/parcels/tools/converters.py b/parcels/tools/converters.py
@@ -10,15 +10,15 @@
 import xarray as xr
 
 __all__ = [
-    "UnitConverter",
     "Geographic",
     "GeographicPolar",
-    "GeographicSquare",
     "GeographicPolarSquare",
-    "unitconverters_map",
+    "GeographicSquare",
     "TimeConverter",
-    "convert_xarray_time_units",
+    "UnitConverter",
     "convert_to_flat_array",
+    "convert_xarray_time_units",
+    "unitconverters_map",
 ]
 
 
diff --git a/parcels/tools/global_statics.py b/parcels/tools/global_statics.py
@@ -15,7 +15,7 @@
     USER_ID = "tmp"
 
 
-__all__ = ["cleanup_remove_files", "cleanup_unload_lib", "get_package_dir", "get_cache_dir"]
+__all__ = ["cleanup_remove_files", "cleanup_unload_lib", "get_cache_dir", "get_package_dir"]
 
 
 def cleanup_remove_files(lib_file, log_file):
diff --git a/parcels/tools/statuscodes.py b/parcels/tools/statuscodes.py
@@ -1,12 +1,12 @@
 """Handling of Errors and particle status codes"""
 
 __all__ = [
-    "StatusCode",
-    "FieldSamplingError",
+    "AllParcelsErrorCodes",
     "FieldOutOfBoundError",
-    "TimeExtrapolationError",
+    "FieldSamplingError",
     "KernelError",
-    "AllParcelsErrorCodes",
+    "StatusCode",
+    "TimeExtrapolationError",
 ]
 
 
diff --git a/parcels/tools/timer.py b/parcels/tools/timer.py
@@ -43,10 +43,10 @@ def print_tree_sequential(self, step=0, root_time=0, parent_time=0):
         time = self.local_time()
         if step == 0:
             root_time = time
-        print(("(%3d%%)" % round(time / root_time * 100)), end="")
+        print(f"({round(time / root_time * 100):3d}%)", end="")
         print("  " * (step + 1), end="")
         if step > 0:
-            print("(%3d%%) " % round(time / parent_time * 100), end="")
+            print(f"({round(time / parent_time * 100):3d}%) ", end="")
         t_str = f"{time:1.3e} s" if root_time < 300 else datetime.timedelta(seconds=time)
         print(f"Timer {(self._name).ljust(20 - 2*step + 7*(step == 0))}: {t_str}")
         for child in self._children:
@@ -64,6 +64,6 @@ def print_tree(self, step=0, root_time=0, parent_time=0):
             else:
                 for iproc in range(mpi_size):
                     if iproc == mpi_rank:
-                        print("Proc %d/%d - Timer tree" % (mpi_rank, mpi_size))
+                        print(f"Proc {mpi_rank}/{mpi_size} - Timer tree")
                         self.print_tree_sequential(step, root_time, parent_time)
                     mpi_comm.Barrier()
diff --git a/tests/test_kernel_language.py b/tests/test_kernel_language.py
@@ -276,7 +276,7 @@ def test_print(fieldset_unit_mesh, mode, capfd):
     def kernel(particle, fieldset, time):
         particle.p = 1e-3
         tmp = 5
-        print("%d %f %f" % (particle.id, particle.p, tmp))
+        print(f"{particle.id} {particle.p:f} {tmp:f}")
 
     pset.execute(kernel, endtime=1.0, dt=1.0, verbose_progress=False)
     out, err = capfd.readouterr()
diff --git a/tests/test_mpirun.py b/tests/test_mpirun.py
@@ -19,13 +19,10 @@ def test_mpi_run(tmpdir, repeatdt, maxage, nump):
     outputNoMPI = tmpdir.join("StommelNoMPI.zarr")
 
     os.system(
-        "mpirun -np 2 python %s -p %d -o %s -r %d -a %d -wf False -cpf True"
-        % (stommel_file, nump, outputMPI_partition_function, repeatdt, maxage)
+        f"mpirun -np 2 python {stommel_file} -p {nump} -o {outputMPI_partition_function} -r {repeatdt} -a {maxage} -wf False -cpf True"
     )
-    os.system(
-        "mpirun -np 2 python %s -p %d -o %s -r %d -a %d -wf False" % (stommel_file, nump, outputMPI, repeatdt, maxage)
-    )
-    os.system("python %s -p %d -o %s -r %d -a %d -wf False" % (stommel_file, nump, outputNoMPI, repeatdt, maxage))
+    os.system(f"mpirun -np 2 python {stommel_file} -p {nump} -o {outputMPI} -r {repeatdt} -a {maxage} -wf False")
+    os.system(f"python {stommel_file} -p {nump} -o {outputNoMPI} -r {repeatdt} -a {maxage} -wf False")
 
     ds2 = xr.open_zarr(outputNoMPI)
 

Original file line number	Diff line number	Diff line change
`@@ -247,7 +247,7 @@ def test_pop(mode, chunk_mode):`
`247`	`247`	`filenames = str(data_folder / "t.x1_SAMOC_flux.1690*.nc")`
`248`	`248`	`variables = {"U": "UVEL", "V": "VVEL", "W": "WVEL"}`
`249`	`249`	`timestamps = np.expand_dims(`
`250`		`- np.array([np.datetime64("2000-%.2d-01" % m) for m in range(1, 7)]), axis=1`
	`250`	`+ np.array([np.datetime64(f"2000-{m:02d}-01") for m in range(1, 7)]), axis=1`
`251`	`251`	`)`
`252`	`252`	`dimensions = {"lon": "ULON", "lat": "ULAT", "depth": "w_dep"}`
`253`	`253`	`chs = False`
Original file line number	Diff line number	Diff line change
`@@ -168,7 +168,7 @@ def peninsula_example(`
`168`	`168`	`out = (`
`169`	`169`	`pset.ParticleFile(name=outfile, outputdt=timedelta(hours=1)) if output else None`
`170`	`170`	`)`
`171`		`- print("Peninsula: Advecting %d particles for %s" % (npart, str(time)))`
	`171`	`+ print(f"Peninsula: Advecting {npart} particles for {time}")`
`172`	`172`	`pset.execute(k_adv + k_p, runtime=time, dt=dt, output_file=out)`
`173`	`173`
`174`	`174`	`if verbose:`