Merge pull request #1680 from OceanParcels/v/small-changes

Enable pyupgrade, add Grid repr, and other changes

.binder/environment.yml

@@ -1,6 +1,5 @@
 name: parcels_binder
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - parcels

docs/documentation/additional_examples.rst

@@ -1,3 +1,6 @@
+Python Example Scripts
+======================
+
 example_brownian.py
 -------------------
 

docs/examples/tutorial_delaystart.ipynb

@@ -76,7 +76,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The simplest way to delaye the start of a particle is to use the `time` argument for each particle\n"
+    "The simplest way to delay the start of a particle is to use the `time` argument for each particle\n"
    ]
   },
   {

docs/examples/tutorial_timestamps.ipynb

@@ -127,7 +127,7 @@
    "outputs": [],
    "source": [
     "timestamps = np.expand_dims(\n",
-    "    np.array([np.datetime64(\"2001-%.2d-15\" % m) for m in range(1, 13)]), axis=1\n",
+    "    np.array([np.datetime64(f\"2001-{m:02d}-15\") for m in range(1, 13)]), axis=1\n",
     ")"
    ]
   },

docs/examples/tutorial_unitconverters.ipynb

@@ -280,7 +280,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The units for Brownian diffusion are in $m^2/s$. If (and only if!) the diffusion fields are called `kh_zonal` and `kh_meridional`, Parcels will automatically assign the correct Unitconverter objects to these fields.\n"
+    "The units for Brownian diffusion are in $m^2/s$. If (and only if!) the diffusion fields are called \"Kh_zonal\" and \"Kh_meridional\", Parcels will automatically assign the correct Unitconverter objects to these fields.\n"
    ]
   },
   {

parcels/_typing.py

@@ -9,7 +9,8 @@
 import ast
 import datetime
 import os
-from typing import Callable, Literal
+from collections.abc import Callable
+from typing import Literal
 
 
 class ParcelsAST(ast.AST):

parcels/compilation/codecompiler.py

@@ -107,7 +107,7 @@ def __init__(self, cppargs=None, ldargs=None, incdirs=None, libdirs=None, libs=N
         self._ldargs += lflags
         self._ldargs += ldargs
         if len(Lflags) > 0:
-            self._ldargs += ["-Wl, -rpath=%s" % (":".join(libdirs))]
+            self._ldargs += [f"-Wl, -rpath={':'.join(libdirs)}"]
         self._ldargs += arch_flag
         self._incdirs = incdirs
         self._libdirs = libdirs

parcels/compilation/codegenerator.py

@@ -33,7 +33,7 @@ def __getattr__(self, attr):
         elif isinstance(getattr(self.obj, attr), VectorField):
             return VectorFieldNode(getattr(self.obj, attr), ccode=f"{self.ccode}->{attr}")
         else:
-            return ConstNode(getattr(self.obj, attr), ccode="%s" % (attr))
+            return ConstNode(getattr(self.obj, attr), ccode=f"{attr}")
 
 
 class FieldNode(IntrinsicNode):
@@ -489,13 +489,13 @@ def visit_FunctionDef(self, node):
             c.Value("double", "time"),
         ]
         for field in self.field_args.values():
-            args += [c.Pointer(c.Value("CField", "%s" % field.ccode_name))]
+            args += [c.Pointer(c.Value("CField", f"{field.ccode_name}"))]
         for field in self.vector_field_args.values():
             for fcomponent in ["U", "V", "W"]:
                 try:
                     f = getattr(field, fcomponent)
                     if f.ccode_name not in self.field_args:
-                        args += [c.Pointer(c.Value("CField", "%s" % f.ccode_name))]
+                        args += [c.Pointer(c.Value("CField", f"{f.ccode_name}"))]
                         self.field_args[f.ccode_name] = f
                 except:
                     pass  # field.W does not always exist
@@ -528,9 +528,9 @@ def visit_Call(self, node):
         if isinstance(node.func, PrintNode):
             # Write our own Print parser because Python3-AST does not seem to have one
             if isinstance(node.args[0], ast.Str):
-                node.ccode = str(c.Statement('printf("%s\\n")' % (node.args[0].s)))
+                node.ccode = str(c.Statement(f'printf("{node.args[0].s}\\n")'))
             elif isinstance(node.args[0], ast.Name):
-                node.ccode = str(c.Statement('printf("%%f\\n", %s)' % (node.args[0].id)))
+                node.ccode = str(c.Statement(f'printf("%f\\n", {node.args[0].id})'))
             elif isinstance(node.args[0], ast.BinOp):
                 if hasattr(node.args[0].right, "ccode"):
                     args = node.args[0].right.ccode
@@ -545,12 +545,12 @@ def visit_Call(self, node):
                             args.append(a.id)
                 else:
                     args = []
-                s = 'printf("%s\\n"' % node.args[0].left.s
+                s = f'printf("{node.args[0].left.s}\\n"'
                 if isinstance(args, str):
-                    s = s + (", %s)" % args)
+                    s = s + f", {args})"
                 else:
                     for arg in args:
-                        s = s + (", %s" % arg)
+                        s = s + (f", {arg}")
                     s = s + ")"
                 node.ccode = str(c.Statement(s))
             else:
@@ -568,7 +568,7 @@ def visit_Call(self, node):
                 elif isinstance(a, ParticleNode):
                     continue
                 elif pointer_args:
-                    a.ccode = "&%s" % a.ccode
+                    a.ccode = f"&{a.ccode}"
             ccode_args = ", ".join([a.ccode for a in node.args[pointer_args:]])
             try:
                 if isinstance(node.func, str):
@@ -742,7 +742,7 @@ def visit_BoolOp(self, node):
         self.visit(node.op)
         for v in node.values:
             self.visit(v)
-        op_str = " %s " % node.op.ccode
+        op_str = f" {node.op.ccode} "
         node.ccode = op_str.join([v.ccode for v in node.values])
 
     def visit_Eq(self, node):
@@ -813,7 +813,7 @@ def visit_ConstNode(self, node):
 
     def visit_Return(self, node):
         self.visit(node.value)
-        node.ccode = c.Statement("return %s" % node.value.ccode)
+        node.ccode = c.Statement(f"return {node.value.ccode}")
 
     def visit_FieldEvalNode(self, node):
         self.visit(node.field)
@@ -909,16 +909,16 @@ def visit_Print(self, node):
         for n in node.values:
             self.visit(n)
         if hasattr(node.values[0], "s"):
-            node.ccode = c.Statement('printf("%s\\n")' % (n.ccode))
+            node.ccode = c.Statement(f'printf("{n.ccode}\\n")')
             return
         if hasattr(node.values[0], "s_print"):
             args = node.values[0].right.ccode
-            s = 'printf("%s\\n"' % node.values[0].left.ccode
+            s = f'printf("{node.values[0].left.ccode}\\n"'
             if isinstance(args, str):
-                s = s + (", %s)" % args)
+                s = s + f", {args})"
             else:
                 for arg in args:
-                    s = s + (", %s" % arg)
+                    s = s + (f", {arg}")
                 s = s + ")"
             node.ccode = c.Statement(s)
             return
@@ -973,7 +973,7 @@ def generate(self, funcname, field_args, const_args, kernel_ast, c_include):
             c.Value("double", "dt"),
         ]
         for field, _ in field_args.items():
-            args += [c.Pointer(c.Value("CField", "%s" % field))]
+            args += [c.Pointer(c.Value("CField", f"{field}"))]
         for const, _ in const_args.items():
             args += [c.Value("double", const)]  # are we SURE those const's are double's ?
         fargs_str = ", ".join(["particles->time_nextloop[pnum]"] + list(field_args.keys()) + list(const_args.keys()))

parcels/field.py

@@ -2,9 +2,10 @@
 import datetime
 import math
 import warnings
+from collections.abc import Iterable
 from ctypes import POINTER, Structure, c_float, c_int, pointer
 from pathlib import Path
-from typing import TYPE_CHECKING, Iterable, Type
+from typing import TYPE_CHECKING
 
 import dask.array as da
 import numpy as np
@@ -222,7 +223,7 @@ def __init__(
                 stacklevel=2,
             )
 
-        self.fieldset: "FieldSet" | None = None
+        self.fieldset: FieldSet | None = None
         if allow_time_extrapolation is None:
             self.allow_time_extrapolation = True if len(self.grid.time) == 1 else False
         else:
@@ -299,7 +300,7 @@ def __init__(
         # since some datasets do not provide the deeper level of data (which is ignored by the interpolation).
         self.data_full_zdim = kwargs.pop("data_full_zdim", None)
         self.data_chunks = []  # type: ignore # the data buffer of the FileBuffer raw loaded data - shall be a list of C-contiguous arrays
-        self.c_data_chunks: list["PointerType" | None] = []  # C-pointers to the data_chunks array
+        self.c_data_chunks: list[PointerType | None] = []  # C-pointers to the data_chunks array
         self.nchunks: tuple[int, ...] = ()
         self.chunk_set: bool = False
         self.filebuffers = [None] * 2
@@ -565,13 +566,10 @@ def from_netcdf(
                 "time dimension in indices is not necessary anymore. It is then ignored.", FieldSetWarning, stacklevel=2
             )
 
-        if "full_load" in kwargs:  # for backward compatibility with Parcels < v2.0.0
-            deferred_load = not kwargs["full_load"]
-
-        if grid.time.size <= 2 or deferred_load is False:
+        if grid.time.size <= 2:
             deferred_load = False
 
-        _field_fb_class: Type[DeferredDaskFileBuffer | DaskFileBuffer | DeferredNetcdfFileBuffer | NetcdfFileBuffer]
+        _field_fb_class: type[DeferredDaskFileBuffer | DaskFileBuffer | DeferredNetcdfFileBuffer | NetcdfFileBuffer]
         if chunksize not in [False, None]:
             if deferred_load:
                 _field_fb_class = DeferredDaskFileBuffer
@@ -828,11 +826,9 @@ def calc_cell_edge_sizes(self):
                 self.cell_edge_sizes = self.grid.cell_edge_sizes
             else:
                 raise ValueError(
-                    (
-                        f"Field.cell_edge_sizes() not implemented for {self.grid.gtype} grids. "
-                        "You can provide Field.grid.cell_edge_sizes yourself by in, e.g., "
-                        "NEMO using the e1u fields etc from the mesh_mask.nc file."
-                    )
+                    f"Field.cell_edge_sizes() not implemented for {self.grid.gtype} grids. "
+                    "You can provide Field.grid.cell_edge_sizes yourself by in, e.g., "
+                    "NEMO using the e1u fields etc from the mesh_mask.nc file."
                 )
 
     def cell_areas(self):

parcels/fieldset.py

@@ -1228,7 +1228,7 @@ def from_parcels(
         extra_fields.update({"U": uvar, "V": vvar})
         for vars in extra_fields:
             dimensions[vars] = deepcopy(default_dims)
-            dimensions[vars]["depth"] = "depth%s" % vars.lower()
+            dimensions[vars]["depth"] = f"depth{vars.lower()}"
         filenames = {v: str(f"{basename}{v}.nc") for v in extra_fields.keys()}
         return cls.from_netcdf(
             filenames,
@@ -1317,7 +1317,7 @@ def from_modulefile(cls, filename, modulename="create_fieldset", **kwargs):
         """
         # check if filename exists
         if not os.path.exists(filename):
-            raise IOError(f"FieldSet module file {filename} does not exist")
+            raise OSError(f"FieldSet module file {filename} does not exist")
 
         # Importing the source file directly (following https://docs.python.org/3/library/importlib.html#importing-a-source-file-directly)
         spec = importlib.util.spec_from_file_location(modulename, filename)
@@ -1326,10 +1326,10 @@ def from_modulefile(cls, filename, modulename="create_fieldset", **kwargs):
         spec.loader.exec_module(fieldset_module)
 
         if not hasattr(fieldset_module, modulename):
-            raise IOError(f"{filename} does not contain a {modulename} function")
+            raise OSError(f"{filename} does not contain a {modulename} function")
         fieldset = getattr(fieldset_module, modulename)(**kwargs)
         if not isinstance(fieldset, FieldSet):
-            raise IOError(f"Module {filename}.{modulename} does not return a FieldSet object")
+            raise OSError(f"Module {filename}.{modulename} does not return a FieldSet object")
         return fieldset
 
     def get_fields(self):

parcels/grid.py

@@ -92,6 +92,14 @@ def __init__(
         self._add_last_periodic_data_timestep = False
         self.depth_field = None
 
+    def __repr__(self):
+        with np.printoptions(threshold=5, suppress=True, linewidth=120, formatter={"float": "{: 0.2f}".format}):
+            return (
+                f"{type(self).__name__}("
+                f"lon={self.lon!r}, lat={self.lat!r}, time={self.time!r}, "
+                f"time_origin={self.time_origin!r}, mesh={self.mesh!r})"
+            )
+
     @staticmethod
     def create_grid(
         lon: npt.ArrayLike,
@@ -352,7 +360,7 @@ def __init__(self, lon, lat, time, time_origin, mesh: Mesh):
                 stacklevel=2,
             )
 
-    def add_periodic_halo(self, zonal, meridional, halosize=5):
+    def add_periodic_halo(self, zonal: bool, meridional: bool, halosize: int = 5):
         """Add a 'halo' to the Grid, through extending the Grid (and lon/lat)
         similarly to the halo created for the Fields
 

parcels/interaction/interactionkernel.py

@@ -1,5 +1,4 @@
 import inspect
-import sys
 import warnings
 from collections import defaultdict
 
@@ -109,10 +108,7 @@ def check_kernel_signature_on_version(self):
         numkernelargs = []
         if self._pyfunc is not None and isinstance(self._pyfunc, list):
             for func in self._pyfunc:
-                if sys.version_info[0] < 3:
-                    numkernelargs.append(len(inspect.getargspec(func).args))
-                else:
-                    numkernelargs.append(len(inspect.getfullargspec(func).args))
+                numkernelargs.append(len(inspect.getfullargspec(func).args))
         return numkernelargs
 
     def remove_lib(self):

parcels/kernel.py

@@ -127,7 +127,7 @@ def _cache_key(self):
             field_keys = "-".join(
                 [f"{name}:{field.units.__class__.__name__}" for name, field in self.field_args.items()]
             )
-        key = self.name + self.ptype._cache_key + field_keys + ("TIME:%f" % ostime())
+        key = self.name + self.ptype._cache_key + field_keys + (f"TIME:{ostime():f}")
         return hashlib.md5(key.encode("utf-8")).hexdigest()
 
     def remove_deleted(self, pset):
@@ -239,9 +239,10 @@ def __init__(
 
         numkernelargs = self.check_kernel_signature_on_version()
 
-        assert (
-            numkernelargs == 3
-        ), "Since Parcels v2.0, kernels do only take 3 arguments: particle, fieldset, time !! AND !! Argument order in field interpolation is time, depth, lat, lon."
+        if numkernelargs != 3:
+            raise ValueError(
+                "Since Parcels v2.0, kernels do only take 3 arguments: particle, fieldset, time !! AND !! Argument order in field interpolation is time, depth, lat, lon."
+            )
 
         self.name = f"{ptype.name}{self.funcname}"
 
@@ -310,7 +311,7 @@ def _cache_key(self):
             field_keys = "-".join(
                 [f"{name}:{field.units.__class__.__name__}" for name, field in self.field_args.items()]
             )
-        key = self.name + self.ptype._cache_key + field_keys + ("TIME:%f" % ostime())
+        key = self.name + self.ptype._cache_key + field_keys + (f"TIME:{ostime():f}")
         return hashlib.md5(key.encode("utf-8")).hexdigest()
 
     def add_scipy_positionupdate_kernels(self):
@@ -330,7 +331,7 @@ def Updatecoords(particle, fieldset, time):
             particle.depth_nextloop = particle.depth + particle_ddepth  # noqa
             particle.time_nextloop = particle.time + particle.dt
 
-        self._pyfunc = self.__radd__(Setcoords).__add__(Updatecoords)._pyfunc
+        self._pyfunc = (Setcoords + self + Updatecoords)._pyfunc
 
     def check_fieldsets_in_kernels(self, pyfunc):
         """
@@ -396,13 +397,10 @@ def check_fieldsets_in_kernels(self, pyfunc):
                     self.fieldset.add_constant("RK45_max_dt", 60 * 60 * 24)
 
     def check_kernel_signature_on_version(self):
-        numkernelargs = 0
-        if self._pyfunc is not None:
-            if sys.version_info[0] < 3:
-                numkernelargs = len(inspect.getargspec(self._pyfunc).args)
-            else:
-                numkernelargs = len(inspect.getfullargspec(self._pyfunc).args)
-        return numkernelargs
+        """Returns number of arguments in a Python function."""
+        if self._pyfunc is None:
+            return 0
+        return len(inspect.getfullargspec(self._pyfunc).args)
 
     def remove_lib(self):
         if self._lib is not None:
@@ -449,7 +447,7 @@ def get_kernel_compile_files(self):
                 self._cache_key
             )  # only required here because loading is done by Kernel class instead of Compiler class
             dyn_dir = get_cache_dir()
-            basename = "%s_0" % cache_name
+            basename = f"{cache_name}_0"
         lib_path = "lib" + basename
         src_file_or_files = None
         if type(basename) in (list, dict, tuple, ndarray):