Added many flake8 checks in ruff (#597)

* Added many `flake8` checks in `ruff`
* Did a lot of fixes to pass the additional tests
* Updated documentation on code style

docs/source/conf.py

@@ -15,9 +15,9 @@
 import sys
 
 sys.path.insert(0, ".")
-sys.path.insert(0, os.path.abspath("../.."))
-sys.path.insert(0, os.path.abspath("../../scripts"))
-sys.path.insert(0, os.path.abspath("../sphinx_ext/"))
+sys.path.insert(0, os.path.abspath("../.."))  # noqa: PTH100
+sys.path.insert(0, os.path.abspath("../../scripts"))  # noqa: PTH100
+sys.path.insert(0, os.path.abspath("../sphinx_ext/"))  # noqa: PTH100
 
 from datetime import date
 
@@ -26,7 +26,7 @@
 project = "py-pde"
 module_name = "pde"
 author = "Zwicker Group"
-copyright = f"{date.today().year}, {author}"  # @ReservedAssignment
+copyright = f"{date.today().year}, {author}"  # @ReservedAssignment  # noqa: A001
 html_logo = "_images/logo_small.png"
 
 # Determine the version from the actual package

docs/source/manual/contributing.rst

@@ -55,8 +55,9 @@ where ``vector_component`` is either 0 or 1.
 
 Coding style
 """"""""""""
-The coding style is enforced using `isort <https://timothycrosley.github.io/isort/>`_
-and `black <https://black.readthedocs.io/>`_. Moreover, we use `Google Style docstrings
+The coding style is enforced using `ruff <https://docs.astral.sh/ruff/>`_, based on the
+styles suggest by `isort <https://timothycrosley.github.io/isort/>`_ and
+`black <https://black.readthedocs.io/>`_. Moreover, we use `Google Style docstrings
 <https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings>`_,
 which might be best `learned by example
 <https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_.

docs/source/run_autodoc.py

@@ -4,6 +4,7 @@
 import logging
 import os
 import subprocess as sp
+from pathlib import Path
 
 logging.basicConfig(level=logging.INFO)
 
@@ -31,21 +32,21 @@ def replace_in_file(infile, replacements, outfile=None):
     if outfile is None:
         outfile = infile
 
-    with open(infile) as fp:
+    with Path(infile).open() as fp:
         content = fp.read()
 
     for key, value in replacements.items():
         content = content.replace(key, value)
 
-    with open(outfile, "w") as fp:
+    with Path(outfile).open("w") as fp:
         fp.write(content)
 
 
 def main():
     # remove old files
-    for path in glob.glob(f"{OUTPUT_PATH}/*.rst"):
+    for path in Path(OUTPUT_PATH).glob("*.rst"):
         logging.info("Remove file `%s`", path)
-        os.remove(path)
+        path.unlink()
 
     # run sphinx-apidoc
     sp.check_call(
@@ -65,7 +66,7 @@ def main():
     )
 
     # replace unwanted information
-    for path in glob.glob(f"{OUTPUT_PATH}/*.rst"):
+    for path in Path(OUTPUT_PATH).glob("*.rst"):
         logging.info("Patch file `%s`", path)
         replace_in_file(path, REPLACEMENTS)
 

examples/pde_brusselator_class.py

@@ -27,11 +27,11 @@
 class BrusselatorPDE(PDEBase):
     """Brusselator with diffusive mobility."""
 
-    def __init__(self, a=1, b=3, diffusivity=[1, 0.1], bc="auto_periodic_neumann"):
+    def __init__(self, a=1, b=3, diffusivity=None, bc="auto_periodic_neumann"):
         super().__init__()
         self.a = a
         self.b = b
-        self.diffusivity = diffusivity  # spatial mobility
+        self.diffusivity = [1, 0.1] if diffusivity is None else diffusivity
         self.bc = bc  # boundary condition
 
     def get_initial_state(self, grid):

pde/__init__.py

@@ -4,7 +4,7 @@
 # determine the package version
 try:
     # try reading version of the automatically generated module
-    from ._version import __version__  # type: ignore
+    from ._version import __version__
 except ImportError:
     # determine version automatically from CVS information
     from importlib.metadata import PackageNotFoundError, version
@@ -20,7 +20,8 @@
 from .tools.config import Config, environment
 
 config = Config()  # initialize the default configuration
-del Config  # clean name space
+
+import contextlib
 
 # import all other modules that should occupy the main name space
 from .fields import *  # @UnusedWildImport
@@ -32,7 +33,7 @@
 from .trackers import *  # @UnusedWildImport
 from .visualization import *  # @UnusedWildImport
 
-try:
+with contextlib.suppress(ImportError):
     from .tools.modelrunner import *
-except ImportError:
-    pass  # modelrunner extensions are simply not loaded
+
+del contextlib, Config  # clean name space

pde/fields/datafield_base.py

@@ -1131,7 +1131,7 @@ def get_vector_data(self, transpose: bool = False, **kwargs) -> dict[str, Any]:
         Returns:
             dict: Information useful for plotting an vector field
         """
-        raise NotImplementedError()
+        raise NotImplementedError
 
     def _plot_line(
         self,

pde/fields/scalar.py

@@ -372,7 +372,7 @@ def slice(
                 raise ValueError(
                     f"The axes {ax} is not contained in "
                     f"{self.grid} with axes {self.grid.axes}"
-                )
+                ) from None
             ax_remove.append(i)
 
             # check the position

pde/fields/tensorial.py

@@ -124,8 +124,8 @@ def _get_axes_index(self, key: tuple[int | str, int | str]) -> tuple[int, int]:
         try:
             if len(key) != 2:
                 raise IndexError("Index must be given as two integers")
-        except TypeError:
-            raise IndexError("Index must be given as two values")
+        except TypeError as err:
+            raise IndexError("Index must be given as two values") from err
         return tuple(self.grid.get_axis_index(k) for k in key)  # type: ignore
 
     def __getitem__(self, key: tuple[int | str, int | str]) -> ScalarField:

pde/fields/vectorial.py

@@ -317,8 +317,8 @@ def check_rank(arr: nb.types.Type | nb.types.Optional) -> None:
             @register_jitable
             def calc(a: np.ndarray, b: np.ndarray, out: np.ndarray) -> np.ndarray:
                 """Calculate outer product between fields `a` and `b`"""
-                for i in range(0, dim):
-                    for j in range(0, dim):
+                for i in range(dim):
+                    for j in range(dim):
                         out[i, j, :] = a[i] * b[j]
                 return out
 

pde/grids/base.py

@@ -1021,7 +1021,7 @@ def contains_point(
             the grid
         """
         cell_coords = self.transform(points, source=coords, target="cell", full=full)
-        return np.all((0 <= cell_coords) & (cell_coords <= self.shape), axis=-1)  # type: ignore
+        return np.all((cell_coords >= 0) & (cell_coords <= self.shape), axis=-1)  # type: ignore
 
     def iter_mirror_points(
         self, point: np.ndarray, with_self: bool = False, only_periodic: bool = True
@@ -1222,6 +1222,7 @@ def register_operator(factor_func_arg: OperatorFactory):
         else:
             # method is used directly
             register_operator(factory_func)
+            return None
 
     @hybridmethod  # type: ignore
     @property

pde/grids/boundaries/axes.py

@@ -264,7 +264,7 @@ def __setitem__(self, index, data) -> None:
 
         else:
             # handle all other cases, in particular integer indices
-            return super().__setitem__(index, data)
+            super().__setitem__(index, data)
 
     def get_mathematical_representation(self, field_name: str = "C") -> str:
         """Return mathematical representation of the boundary condition."""
@@ -303,7 +303,7 @@ def set_ghost_cells(
                 for i, j in itertools.product([0, -1], [0, -1]):
                     d[..., i, j] = (d[..., nxt[i], j] + d[..., i, nxt[j]]) / 2
 
-            elif self.grid.num_axes >= 3:
+            elif self.grid.num_axes == 3:
                 # iterate all edges
                 for i, j in itertools.product([0, -1], [0, -1]):
                     d[..., :, i, j] = (+d[..., :, nxt[i], j] + d[..., :, i, nxt[j]]) / 2
@@ -316,8 +316,9 @@ def set_ghost_cells(
                         + d[..., i, nxt[j], k]
                         + d[..., i, j, nxt[k]]
                     ) / 3
-            else:
-                logging.getLogger(self.__class__.__name__).warning(
+
+            elif self.grid.num_axes > 3:
+                raise NotImplementedError(
                     f"Can't interpolate corners for grid with {self.grid.num_axes} axes"
                 )
 

pde/grids/boundaries/axis.py

@@ -287,7 +287,7 @@ def from_data(cls, grid: GridBase, axis: int, data, rank: int = 0) -> BoundaryPa
                 # if len is not supported, the format must be wrong
                 raise BCDataError(
                     f"Unsupported boundary format: `{data}`. " + cls.get_help()
-                )
+                ) from None
             else:
                 if data_len == 2:
                     # assume that data is given for each boundary

pde/grids/boundaries/local.py

@@ -426,7 +426,7 @@ def from_str(
         except KeyError:
             raise BCDataError(
                 f"Boundary condition `{condition}` not defined. " + cls.get_help()
-            )
+            ) from None
 
         # create the actual class
         return boundary_class(grid=grid, axis=axis, upper=upper, rank=rank, **kwargs)
@@ -459,7 +459,7 @@ def from_dict(
         data = data.copy()  # need to make a copy since we modify it below
 
         # parse all possible variants that could be given
-        if "type" in data.keys():
+        if "type" in data:
             # type is given (optionally with a value)
             b_type = data.pop("type")
             return cls.from_str(grid, axis, upper, condition=b_type, rank=rank, **data)
@@ -1224,14 +1224,13 @@ def __init__(
         except Exception as err:
             if self._is_func:
                 raise BCDataError(
-                    f"Could not evaluate BC function. Expected signature "
-                    f"{signature}.\nEncountered error: {err}"
-                )
+                    f"Could not evaluate BC function. Expected signature {signature}."
+                ) from err
             else:
                 raise BCDataError(
                     f"Could not evaluate BC expression `{expression}` with signature "
-                    f"{signature}.\nEncountered error: {err}"
-                )
+                    f"{signature}."
+                ) from err
 
     @property
     def _test_values(self) -> tuple[float, ...]:
@@ -1275,7 +1274,7 @@ def value_func(*args):
 
             except nb.NumbaError:
                 # if compilation fails, we simply fall back to pure-python mode
-                self._logger.warning(f"Cannot compile BC {self}")
+                self._logger.warning("Cannot compile BC %s", self)
 
                 @register_jitable
                 def value_func(*args):
@@ -1360,7 +1359,7 @@ def _get_function_from_expression(self, do_jit: bool) -> Callable:
 
         except nb.NumbaError:
             # if compilation fails, we simply fall back to pure-python mode
-            self._logger.warning(f"Cannot compile BC {self._func_expression}")
+            self._logger.warning("Cannot compile BC %s", self._func_expression)
             # calculate the expected value to test this later (and fail early)
             expected = func(*self._test_values)
 
@@ -1391,12 +1390,14 @@ def value_func(grid_value, dx, x, y, z, t):
 
             else:
                 # cheap way to signal a problem
-                raise ValueError
+                raise ValueError from None
 
             # compile the actual functio and check the result
             result_compiled = value_func(*self._test_values)
             if not np.allclose(result_compiled, expected):
-                raise RuntimeError("Compiled function does not give same value")
+                raise RuntimeError(
+                    "Compiled function does not give same value"
+                ) from None
 
         return value_func  # type: ignore
 
@@ -2974,4 +2975,4 @@ def registered_boundary_condition_names() -> dict[str, type[BCBase]]:
     Returns:
         dict: a dictionary with the names of the boundary conditions that can be used
     """
-    return {cls_name: cls for cls_name, cls in BCBase._conditions.items()}
+    return dict(BCBase._conditions.items())

pde/grids/cartesian.py

@@ -319,7 +319,7 @@ def _get_axis(axis):
                 try:
                     axis = self.axes.index(axis)
                 except ValueError:
-                    raise ValueError(f"Axis `{axis}` not defined")
+                    raise ValueError(f"Axis `{axis}` not defined") from None
             return axis
 
         if extract == "auto":

pde/grids/operators/cartesian.py

@@ -986,7 +986,8 @@ def _make_divergence_scipy_nd(
 
     def divergence(arr: np.ndarray, out: np.ndarray) -> None:
         """Apply divergence operator to array `arr`"""
-        assert arr.shape[0] == len(data_shape) and arr.shape[1:] == data_shape
+        assert arr.shape[0] == len(data_shape)
+        assert arr.shape[1:] == data_shape
 
         # need to initialize with zeros since data is added later
         if out is None:

pde/grids/operators/polar_sym.py

@@ -300,12 +300,11 @@ def _get_laplace_matrix(bcs: Boundaries) -> tuple[np.ndarray, np.ndarray]:
             if r_min == 0:
                 matrix[i, i + 1] = 2 * scale
                 continue  # the special case of the inner boundary is handled
-            else:
-                const, entries = bcs[0].get_sparse_matrix_data((-1,))
-                factor = scale - scale_i
-                vector[i] += const * factor
-                for k, v in entries.items():
-                    matrix[i, k] += v * factor
+            const, entries = bcs[0].get_sparse_matrix_data((-1,))
+            factor = scale - scale_i
+            vector[i] += const * factor
+            for k, v in entries.items():
+                matrix[i, k] += v * factor
 
         else:
             matrix[i, i - 1] = scale - scale_i

pde/grids/operators/spherical_sym.py

@@ -57,7 +57,8 @@ def make_laplace(grid: SphericalSymGrid, *, conservative: bool = True) -> Operat
         # create a conservative spherical laplace operator
         rl = rs - dr / 2  # inner radii of spherical shells
         rh = rs + dr / 2  # outer radii
-        assert np.isclose(rl[0], r_min) and np.isclose(rh[-1], r_max)
+        assert np.isclose(rl[0], r_min)
+        assert np.isclose(rh[-1], r_max)
         volumes = (rh**3 - rl**3) / 3  # volume of the spherical shells
         factor_l = rl**2 / (dr * volumes)
         factor_h = rh**2 / (dr * volumes)
@@ -496,7 +497,8 @@ def make_tensor_double_divergence(
         rl = rs - dr / 2  # inner radii of spherical shells
         rh = rs + dr / 2  # outer radii
         r_min, r_max = grid.axes_bounds[0]
-        assert np.isclose(rl[0], r_min) and np.isclose(rh[-1], r_max)
+        assert np.isclose(rl[0], r_min)
+        assert np.isclose(rh[-1], r_max)
         volumes = (rh**3 - rl**3) / 3  # volume of the spherical shells
         factor_l = rl / volumes
         factor_h = rh / volumes

pde/pdes/base.py

@@ -447,7 +447,6 @@ def noise_realization(state_data: np.ndarray, t: float) -> np.ndarray:
             @jit
             def noise_realization(state_data: np.ndarray, t: float) -> None:
                 """Helper function returning a noise realization."""
-                return None
 
         return noise_realization  # type: ignore
 

pde/pdes/laplace.py

@@ -65,14 +65,14 @@ def solve_poisson_equation(
     result = ScalarField(rhs.grid, label=label)
     try:
         solver(rhs.data, result.data)
-    except RuntimeError:
+    except RuntimeError as err:
         magnitude = rhs.magnitude
         if magnitude > 1e-10:
             raise RuntimeError(
                 "Could not solve the Poisson problem. One possible reason for this is "
                 "that only periodic or Neumann conditions are applied although the "
                 f"magnitude of the field is {magnitude} and thus non-zero."
-            )
+            ) from err
         else:
             raise  # another error occurred