code formatting updates to match changes in black requirements (#420)

.pre-commit-config.yaml

@@ -4,18 +4,18 @@ default_stages: [commit]
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 24.1.1
     hooks:
       - id: black
 
   - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black"]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

PyMPDATA/__init__.py

@@ -7,6 +7,7 @@
 `PyMPDATA.vector_field.VectorField` elements:
 ![](https://github.com/atmos-cloud-sim-uj/PyMPDATA/releases/download/tip/readme_grid.png)
 """
+
 # pylint: disable=invalid-name
 from importlib.metadata import PackageNotFoundError, version
 

PyMPDATA/boundary_conditions/__init__.py

@@ -1,4 +1,5 @@
 """ classes representing boundary conditions """
+
 from .constant import Constant
 from .extrapolated import Extrapolated
 from .periodic import Periodic

PyMPDATA/boundary_conditions/constant.py

@@ -1,4 +1,5 @@
 """ boundary condition filling halos with a constant value """
+
 # pylint: disable=too-many-arguments
 from functools import lru_cache
 

PyMPDATA/boundary_conditions/extrapolated.py

@@ -1,6 +1,7 @@
 """ boundary condition extrapolating values from the edge to the halo for scalars
 and returning edge-of-the-domain value for vectors (with all negative scalar values
 set to zero) """
+
 # pylint: disable=too-many-arguments
 from functools import lru_cache
 

PyMPDATA/boundary_conditions/periodic.py

@@ -1,4 +1,5 @@
 """ periodic/cyclic boundary condition logic """
+
 from functools import lru_cache
 
 import numba

PyMPDATA/boundary_conditions/polar.py

@@ -1,4 +1,5 @@
 """ polar boundary condition for use in with spherical coordinates """
+
 from functools import lru_cache
 
 import numba

PyMPDATA/impl/clock.py

@@ -1,5 +1,6 @@
 """ CPU-time returning clock() function which works from within njit-ted code,
     no time unit guaranteed, returned value only for relative time measurements """
+
 import ctypes
 
 clock = ctypes.pythonapi._PyTime_GetSystemClock  # pylint:disable=protected-access

PyMPDATA/impl/domain_decomposition.py

@@ -1,4 +1,5 @@
 """ logic defining domain decomposition scheme for multi-threading """
+
 import math
 
 import numba

PyMPDATA/impl/enumerations.py

@@ -1,4 +1,5 @@
 """ common constants (mostly integer indices used for indexing tuples) """
+
 import numpy as np
 
 ARG_FOCUS, ARG_DATA, ARG_DATA_OUTER, ARG_DATA_MID3D, ARG_DATA_INNER = 0, 1, 1, 2, 3

PyMPDATA/impl/field.py

@@ -1,5 +1,6 @@
 """ common logic for `PyMPDATA.scalar_field.ScalarField` and
  `PyMPDATA.vector_field.VectorField` classes """
+
 import abc
 from collections import namedtuple
 

PyMPDATA/impl/formulae_antidiff.py

@@ -1,5 +1,6 @@
 """ antidiffusive velocity formulae incl. divergent-flow,
     third-order-terms, DPDC and partially also infinite-gauge logic """
+
 import numba
 import numpy as np
 
@@ -12,16 +13,18 @@ def make_antidiff(non_unit_g_factor, options, traversals, last_pass=False):
     apply_vector = traversals.apply_vector()
 
     formulae_antidiff = tuple(
-        __make_antidiff(
-            atv=idx.atv[i],
-            ats=idx.ats[i],
-            non_unit_g_factor=non_unit_g_factor,
-            options=options,
-            n_dims=traversals.n_dims,
-            last_pass=last_pass,
+        (
+            __make_antidiff(
+                atv=idx.atv[i],
+                ats=idx.ats[i],
+                non_unit_g_factor=non_unit_g_factor,
+                options=options,
+                n_dims=traversals.n_dims,
+                last_pass=last_pass,
+            )
+            if idx.ats[i] is not None
+            else None
         )
-        if idx.ats[i] is not None
-        else None
         for i in range(MAX_DIM_NUM)
     )
 

PyMPDATA/impl/formulae_axpy.py

@@ -1,4 +1,5 @@
 """ basic a*x+y operation logic for use in Fickian term handling """
+
 import numba
 
 from .enumerations import INNER, MID3D, OUTER

PyMPDATA/impl/formulae_flux.py

@@ -1,4 +1,5 @@
 """ staggered-grid flux logic including infinite-gauge logic handling """
+
 import numba
 import numpy as np
 
@@ -11,15 +12,17 @@ def make_flux_first_pass(options, traversals):
     apply_vector = traversals.apply_vector()
 
     formulae_flux_first_pass = tuple(
-        __make_flux(
-            options.jit_flags,
-            idx.atv[i],
-            idx.ats[i],
-            first_pass=True,
-            infinite_gauge=False,
+        (
+            __make_flux(
+                options.jit_flags,
+                idx.atv[i],
+                idx.ats[i],
+                first_pass=True,
+                infinite_gauge=False,
+            )
+            if idx.ats[i] is not None
+            else None
         )
-        if idx.ats[i] is not None
-        else None
         for i in range(MAX_DIM_NUM)
     )
 
@@ -47,15 +50,17 @@ def make_flux_subsequent(options, traversals):
     apply_vector = traversals.apply_vector()
 
     formulae_flux_subsequent = tuple(
-        __make_flux(
-            options.jit_flags,
-            idx.atv[i],
-            idx.ats[i],
-            first_pass=False,
-            infinite_gauge=options.infinite_gauge,
+        (
+            __make_flux(
+                options.jit_flags,
+                idx.atv[i],
+                idx.ats[i],
+                first_pass=False,
+                infinite_gauge=options.infinite_gauge,
+            )
+            if idx.ats[i] is not None
+            else None
         )
-        if idx.ats[i] is not None
-        else None
         for i in range(MAX_DIM_NUM)
     )
 

PyMPDATA/impl/formulae_laplacian.py

@@ -1,4 +1,5 @@
 """ logic for handling the Fickian term by modifying physical velocity """
+
 import numba
 
 from ..impl.enumerations import MAX_DIM_NUM
@@ -19,11 +20,13 @@ def apply(_1, _2, _3):
         apply_vector = traversals.apply_vector()
 
         formulae_laplacian = tuple(
-            __make_laplacian(
-                options.jit_flags, idx.ats[i], options.epsilon, non_unit_g_factor
+            (
+                __make_laplacian(
+                    options.jit_flags, idx.ats[i], options.epsilon, non_unit_g_factor
+                )
+                if idx.ats[i] is not None
+                else None
             )
-            if idx.ats[i] is not None
-            else None
             for i in range(MAX_DIM_NUM)
         )
 

PyMPDATA/impl/formulae_nonoscillatory.py

@@ -288,9 +288,11 @@ def apply(_, __, ___):
         apply_vector = traversals.apply_vector()
 
         formulae = tuple(
-            __make_correction(options.jit_flags, idx.ats[i], idx.atv[i])
-            if idx.ats[i] is not None
-            else None
+            (
+                __make_correction(options.jit_flags, idx.ats[i], idx.atv[i])
+                if idx.ats[i] is not None
+                else None
+            )
             for i in range(MAX_DIM_NUM)
         )
 

PyMPDATA/impl/formulae_upwind.py

@@ -1,4 +1,5 @@
 """ upwind/donor-cell formula logic including G-factor handling """
+
 import numba
 
 from PyMPDATA.impl.enumerations import MAX_DIM_NUM
@@ -10,9 +11,11 @@ def make_upwind(options, non_unit_g_factor, traversals):
     idx = traversals.indexers[traversals.n_dims]
 
     formulae_upwind = tuple(
-        __make_upwind(options.jit_flags, idx.atv[i], idx.ats[i], non_unit_g_factor)
-        if idx.ats[i] is not None
-        else None
+        (
+            __make_upwind(options.jit_flags, idx.atv[i], idx.ats[i], non_unit_g_factor)
+            if idx.ats[i] is not None
+            else None
+        )
         for i in range(MAX_DIM_NUM)
     )
 

PyMPDATA/impl/grid.py

@@ -1,6 +1,7 @@
 """
 static (extents known to JIT) and dynamic (run-time extents) grid handling logic
 """
+
 import numba
 
 from PyMPDATA.impl.domain_decomposition import make_subdomain

PyMPDATA/impl/indexers.py

@@ -1,4 +1,5 @@
 """ array indexing logic for 1D, 2D and 3D staggered grids """
+
 # pylint: disable=missing-function-docstring
 
 from collections import namedtuple

PyMPDATA/impl/meta.py

@@ -1,4 +1,5 @@
 """ constants for indexing and a factory for creating the "meta" tuples """
+
 from collections import namedtuple
 from pathlib import Path
 

PyMPDATA/impl/traversals.py

@@ -1,4 +1,5 @@
 """ staggered-grid traversals orchestration """
+
 from collections import namedtuple
 from pathlib import Path
 

PyMPDATA/impl/traversals_common.py

@@ -1,4 +1,5 @@
 """ commons for scalar and vector field traversals """
+
 # pylint: disable=too-many-arguments,line-too-long,unused-argument
 import numba
 

PyMPDATA/impl/traversals_halos_scalar.py

@@ -1,4 +1,5 @@
 """ halo-filling logic for scalar field traversals (incl. multi-threading) """
+
 # pylint: disable=too-many-arguments
 import numba
 

PyMPDATA/impl/traversals_halos_vector.py

@@ -1,4 +1,5 @@
 """ halo-filling logic for vector field traversals (incl. multi-threading) """
+
 # pylint: disable=too-many-statements,too-many-locals,too-many-lines,too-many-function-args,too-many-arguments
 
 import numba

PyMPDATA/impl/traversals_scalar.py

@@ -1,4 +1,5 @@
 """ scalar field traversals (incl. multi-threading) """
+
 import numba
 
 from .enumerations import INNER, INVALID_INDEX, MID3D, RNG_START, RNG_STOP

PyMPDATA/impl/traversals_vector.py

@@ -1,4 +1,5 @@
 """ vector field traversals (incl. multi-threading) """
+
 import numba
 
 from .enumerations import (

PyMPDATA/options.py

@@ -1,6 +1,7 @@
 """
 MPDATA variants, iterations, data-type and jit-flags settings
 """
+
 import numpy as np
 from pystrict import strict
 

PyMPDATA/scalar_field.py

@@ -1,6 +1,7 @@
 """
 scalar field abstractions for the staggered grid
 """
+
 import inspect
 
 import numpy as np

PyMPDATA/solver.py

@@ -2,6 +2,7 @@
 class grouping user-supplied stepper, fields and post-step/post-iter hooks,
 as well as self-initialised temporary storage
 """
+
 from typing import Union
 
 import numba
@@ -71,15 +72,21 @@ def null_vector_field():
             "g_factor": g_factor or null_scalar_field(),
             "vectmp_a": vector_field(),
             "vectmp_b": vector_field(),
-            "vectmp_c": vector_field()
-            if stepper.options.non_zero_mu_coeff
-            else null_vector_field(),
-            "nonosc_xtrm": scalar_field(dtype=complex)
-            if stepper.options.nonoscillatory
-            else null_scalar_field(),
-            "nonosc_beta": scalar_field(dtype=complex)
-            if stepper.options.nonoscillatory
-            else null_scalar_field(),
+            "vectmp_c": (
+                vector_field()
+                if stepper.options.non_zero_mu_coeff
+                else null_vector_field()
+            ),
+            "nonosc_xtrm": (
+                scalar_field(dtype=complex)
+                if stepper.options.nonoscillatory
+                else null_scalar_field()
+            ),
+            "nonosc_beta": (
+                scalar_field(dtype=complex)
+                if stepper.options.nonoscillatory
+                else null_scalar_field()
+            ),
         }
         for field in self.__fields.values():
             field.assemble(stepper.traversals)

PyMPDATA/stepper.py

@@ -1,4 +1,5 @@
 """ MPDATA iteration logic """
+
 import sys
 import warnings
 from functools import lru_cache

PyMPDATA/vector_field.py

@@ -1,6 +1,7 @@
 """
 vector field abstractions for the staggered grid
 """
+
 import inspect
 
 import numpy as np

examples/PyMPDATA_examples/Shipway_and_Hill_2012/settings.py

@@ -69,8 +69,8 @@ def drhod_dz(z, rhod):
         self.rhod = interp1d(z_points, rhod_solution.y[0])
 
         self.t_1 = 600 * si.s
-        self.rhod_w = (
-            lambda t: rhod_w_const * np.sin(np.pi * t / self.t_1) if t < self.t_1 else 0
+        self.rhod_w = lambda t: (
+            rhod_w_const * np.sin(np.pi * t / self.t_1) if t < self.t_1 else 0
         )
 
         self.r_min = r_min

examples/PyMPDATA_examples/__init__.py

@@ -2,6 +2,7 @@
 PyMPDATA_examples package includes common Python modules used in PyMPDATA smoke tests
 and in example notebooks (but the package wheels do not include the notebooks)
 """
+
 from importlib.metadata import PackageNotFoundError, version
 
 try:

examples/setup.py

@@ -1,4 +1,5 @@
 """ the magick behind ``pip install ...`` """
+
 import os
 
 from setuptools import find_packages, setup