Added pre-commit-hook for formatting code (#599)

* Added `pre-commit-hook` for formatting code
* Removed unnecessary comments
* Mentioned pre-commits in documentation

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.3.0
+  hooks:
+    - id: check-yaml
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.1
+  hooks:
+    - id: ruff
+      args: [--fix, --show-fixes]
+    - id: ruff-format

docs/source/conf.py

@@ -26,7 +26,7 @@
 project = "py-pde"
 module_name = "pde"
 author = "Zwicker Group"
-copyright = f"{date.today().year}, {author}"  # @ReservedAssignment  # noqa: A001
+copyright = f"{date.today().year}, {author}"  # noqa: A001
 html_logo = "_images/logo_small.png"
 
 # Determine the version from the actual package

docs/source/manual/contributing.rst

@@ -73,6 +73,7 @@ This folder also contain a script :file:`tests_types.sh`, which uses :mod:`mypy`
 to check the consistency of the python type annotations.
 We use these type annotations for additional documentation and they have also
 already been useful for finding some bugs.
+Finally, we have pre-commit hooks, which you should install using `pre-commit install`.
 
 We also have some conventions that should make the package more consistent and
 thus easier to use. For instance, we try to use ``properties`` instead of getter

pde/__init__.py

@@ -24,14 +24,14 @@
 import contextlib
 
 # import all other modules that should occupy the main name space
-from .fields import *  # @UnusedWildImport
-from .grids import *  # @UnusedWildImport
-from .pdes import *  # @UnusedWildImport
-from .solvers import *  # @UnusedWildImport
-from .storage import *  # @UnusedWildImport
+from .fields import *
+from .grids import *
+from .pdes import *
+from .solvers import *
+from .storage import *
 from .tools.parameters import Parameter
-from .trackers import *  # @UnusedWildImport
-from .visualization import *  # @UnusedWildImport
+from .trackers import *
+from .visualization import *
 
 with contextlib.suppress(ImportError):
     from .tools.modelrunner import *

pde/fields/base.py

@@ -61,7 +61,7 @@ def __init__(
         self.label = label
         self._logger = logging.getLogger(self.__class__.__name__)
 
-    def __init_subclass__(cls, **kwargs):  # @NoSelf
+    def __init_subclass__(cls, **kwargs):
         """Register all subclassess to reconstruct them later."""
         super().__init_subclass__(**kwargs)
 
@@ -359,7 +359,7 @@ def assert_field_compatible(
                 Determines whether it is acceptable that `other` is an instance of
                 :class:`~pde.fields.ScalarField`.
         """
-        from .scalar import ScalarField  # @Reimport
+        from .scalar import ScalarField
 
         # check whether they are the same class
         is_scalar = accept_scalar and isinstance(other, ScalarField)
@@ -489,7 +489,7 @@ def _binary_operation(
 
         if isinstance(other, FieldBase):
             # right operator is a field
-            from .scalar import ScalarField  # @Reimport
+            from .scalar import ScalarField
 
             # determine the dtype of the result of the operation
             dtype = np.result_type(self.data, other.data)
@@ -539,7 +539,7 @@ def _binary_operation_inplace(
         """
         if isinstance(other, FieldBase):
             # right operator is a field
-            from .scalar import ScalarField  # @Reimport
+            from .scalar import ScalarField
 
             if scalar_second:
                 # right operator must be a scalar

pde/fields/collection.py

@@ -1041,9 +1041,7 @@ def plot(
                 kind = [kind] * num_panels
             reference = [
                 field.plot(kind=knd, ax=ax, action="none", **kwargs, **sp_args)
-                for field, knd, ax, sp_args in zip(  # @UnusedVariable
-                    self.fields, kind, axs, subplot_args
-                )
+                for field, knd, ax, sp_args in zip(self.fields, kind, axs, subplot_args)
             ]
 
         # return the references for all subplots

pde/fields/vectorial.py

@@ -205,7 +205,7 @@ def dot(
             :class:`~pde.fields.scalar.ScalarField` or
             :class:`~pde.fields.vectorial.VectorField`: result of applying the operator
         """
-        from .tensorial import Tensor2Field  # @Reimport
+        from .tensorial import Tensor2Field
 
         # check input
         self.grid.assert_grid_compatible(other.grid)
@@ -253,7 +253,7 @@ def outer_product(
         Returns:
             :class:`~pde.fields.tensorial.Tensor2Field`: result of the operation
         """
-        from .tensorial import Tensor2Field  # @Reimport
+        from .tensorial import Tensor2Field
 
         self.assert_field_compatible(other)
 

pde/grids/_mesh.py

@@ -732,7 +732,7 @@ def broadcast(self, data: TData) -> TData:
         Returns:
             The same data, but on all nodes
         """
-        from mpi4py.MPI import COMM_WORLD  # @UnresolvedImport
+        from mpi4py.MPI import COMM_WORLD
 
         return COMM_WORLD.bcast(data, root=0)  # type: ignore
 
@@ -747,7 +747,7 @@ def gather(self, data: TData) -> list[TData] | None:
             None on all nodes, except the main node, which receives an ordered list with
             the data from all nodes.
         """
-        from mpi4py.MPI import COMM_WORLD  # @UnresolvedImport
+        from mpi4py.MPI import COMM_WORLD
 
         return COMM_WORLD.gather(data, root=0)
 
@@ -761,7 +761,7 @@ def allgather(self, data: TData) -> list[TData]:
         Returns:
             list: data from all nodes.
         """
-        from mpi4py.MPI import COMM_WORLD  # @UnresolvedImport
+        from mpi4py.MPI import COMM_WORLD
 
         return COMM_WORLD.allgather(data)
 

pde/grids/base.py

@@ -160,7 +160,7 @@ def __init__(self) -> None:
         self.axes = [self.c.axes[i] for i in self._axes_described]
         self.axes_symmetric = [self.c.axes[i] for i in self.axes_symmetric]  # type: ignore
 
-    def __init_subclass__(cls, **kwargs) -> None:  # @NoSelf
+    def __init_subclass__(cls, **kwargs) -> None:
         """Register all subclassess to reconstruct them later."""
         super().__init_subclass__(**kwargs)
         if cls is not GridBase:
@@ -1066,7 +1066,7 @@ def get_boundary_conditions(
             PeriodicityError:
                 If the boundaries are not compatible with the periodic axes of the grid.
         """
-        from .boundaries import Boundaries  # @Reimport
+        from .boundaries import Boundaries
 
         if self._mesh is None:
             # get boundary conditions for a simple grid that is not part of a mesh
@@ -1226,7 +1226,7 @@ def register_operator(factor_func_arg: OperatorFactory):
 
     @hybridmethod  # type: ignore
     @property
-    def operators(cls) -> set[str]:  # @NoSelf
+    def operators(cls) -> set[str]:
         """set: all operators defined for this class"""
         result = set()
         # add all customly defined operators
@@ -1574,7 +1574,7 @@ def integrate(
 
         else:
             # we are in a parallel run, so we need to gather the sub-integrals from all
-            from mpi4py.MPI import COMM_WORLD  # @UnresolvedImport
+            from mpi4py.MPI import COMM_WORLD
 
             integral_full = np.empty_like(integral)
             COMM_WORLD.Allreduce(integral, integral_full)

pde/grids/boundaries/local.py

@@ -289,7 +289,7 @@ def __init__(self, grid: GridBase, axis: int, upper: bool, *, rank: int = 0):
 
         self._logger = logging.getLogger(self.__class__.__name__)
 
-    def __init_subclass__(cls, **kwargs):  # @NoSelf
+    def __init_subclass__(cls, **kwargs):
         """Register all subclasses to reconstruct them later."""
         super().__init_subclass__(**kwargs)
 

pde/grids/cylindrical.py

@@ -434,7 +434,7 @@ def slice(self, indices: Sequence[int]) -> CartesianGrid | PolarSymGrid:
 
         if indices[0] == 0:
             # return a radial grid
-            from .spherical import PolarSymGrid  # @Reimport
+            from .spherical import PolarSymGrid
 
             return PolarSymGrid(self.radius, self.shape[0])
 

pde/grids/operators/cartesian.py

@@ -28,8 +28,8 @@
 from ...tools.typing import OperatorType
 from ..boundaries import Boundaries
 from ..cartesian import CartesianGrid
-from .common import make_derivative as _make_derivative  # @UnusedImport
-from .common import make_derivative2 as _make_derivative2  # @UnusedImport
+from .common import make_derivative as _make_derivative
+from .common import make_derivative2 as _make_derivative2
 from .common import make_general_poisson_solver, uniform_discretization
 
 # The `make_derivative?` methods are imported for backward compatibility. Their usage is

pde/pdes/base.py

@@ -627,7 +627,7 @@ def solve(
             the current node is not the main MPI node.
         """
         from ..solvers import Controller
-        from ..solvers.base import SolverBase  # @Reimport
+        from ..solvers.base import SolverBase
 
         # create solver instance
         if callable(solver):

pde/pdes/laplace.py

@@ -7,7 +7,7 @@
 
 from ..fields import ScalarField
 from ..grids.base import GridBase
-from ..grids.boundaries.axes import BoundariesData  # @UnusedImport
+from ..grids.boundaries.axes import BoundariesData
 from ..tools.docstrings import fill_in_docstring
 
 

pde/pdes/pde.py

@@ -12,7 +12,7 @@
 
 import numba as nb
 import numpy as np
-from numba.typed import Dict as NumbaDict  # @UnresolvedImport
+from numba.typed import Dict as NumbaDict
 from sympy import Symbol
 from sympy.core.function import UndefinedFunction
 
@@ -329,13 +329,13 @@ def _compile_rhs_single(
             # extend the signature
             signature += tuple(state.grid.axes)
             # inject the spatial coordinates into the expression for the rhs
-            extra_args = tuple(  # @UnusedVariable
+            extra_args = tuple(
                 state.grid.cell_coords[..., i] for i in range(state.grid.num_axes)
             )
 
         else:
             # expression only depends on the actual variables
-            extra_args = ()  # @UnusedVariable
+            extra_args = ()
 
         # check whether all variables are accounted for
         extra_vars = set(expr.vars) - set(signature)

pde/solvers/base.py

@@ -64,7 +64,7 @@ def __init__(self, pde: PDEBase, *, backend: BackendType = "auto"):
             self.info["pde_class"] = self.pde.__class__.__name__
         self._logger = logging.getLogger(self.__class__.__name__)
 
-    def __init_subclass__(cls, **kwargs):  # @NoSelf
+    def __init_subclass__(cls, **kwargs):
         """Register all subclassess to reconstruct them later."""
         super().__init_subclass__(**kwargs)
         if not isabstract(cls):
@@ -113,7 +113,7 @@ def from_name(cls, name: str, pde: PDEBase, **kwargs) -> SolverBase:
         return solver_class(pde, **kwargs)
 
     @classproperty
-    def registered_solvers(cls) -> list[str]:  # @NoSelf
+    def registered_solvers(cls) -> list[str]:
         """list of str: the names of the registered solvers"""
         return sorted(cls._subclasses.keys())
 

pde/storage/base.py

@@ -385,7 +385,7 @@ def extract_field(
             :class:`MemoryStorage`: a storage instance that contains the data for the
             single field
         """
-        from .memory import MemoryStorage  # @Reimport
+        from .memory import MemoryStorage
 
         if self._field is None:
             self._init_field()
@@ -435,7 +435,7 @@ def extract_time_range(
         Returns:
             :class:`MemoryStorage`: a storage instance that contains the extracted data.
         """
-        from .memory import MemoryStorage  # @Reimport
+        from .memory import MemoryStorage
 
         # get the time bracket
         try:
@@ -502,7 +502,7 @@ def apply(
                 raise TypeError("The user function must return a field")
 
             if out is None:
-                from .memory import MemoryStorage  # @Reimport
+                from .memory import MemoryStorage
 
                 out = MemoryStorage(field_obj=transformed)
 
@@ -517,7 +517,7 @@ def apply(
 
         # make sure that a storage is returned, even when no fields are present
         if out is None:
-            from .memory import MemoryStorage  # @Reimport
+            from .memory import MemoryStorage
 
             out = MemoryStorage()
 

pde/tools/cache.py

@@ -281,7 +281,7 @@ def make_unserializer(method: SerializerMethod) -> Callable:
         return yaml.full_load
 
     if method == "yaml_unsafe":
-        import yaml  # @Reimport
+        import yaml
 
         return yaml.unsafe_load
 

pde/tools/expressions.py

@@ -454,7 +454,7 @@ def compile_func(func):
         # partial function instead of replacing the constants in the sympy expression
         # directly since sympy does not work well with numpy arrays.
         if constants:
-            const_values = tuple(self.consts[c] for c in constants)  # @UnusedVariable
+            const_values = tuple(self.consts[c] for c in constants)
 
             if prepare_compilation:
                 func = jit(func)
@@ -1099,13 +1099,11 @@ def evaluate(
         # extend the signature
         signature += tuple(grid.axes)
         # inject the spatial coordinates into the expression for the rhs
-        extra_args = tuple(  # @UnusedVariable
-            grid.cell_coords[..., i] for i in range(grid.num_axes)
-        )
+        extra_args = tuple(grid.cell_coords[..., i] for i in range(grid.num_axes))
 
     else:
         # expression only depends on the actual variables
-        extra_args = ()  # @UnusedVariable
+        extra_args = ()
 
     # check whether all variables are accounted for
     extra_vars = set(expr.vars) - set(signature)

pde/tools/numba.py

@@ -14,7 +14,7 @@
 import numpy as np
 from numba.core.types import npytypes, scalars
 from numba.extending import overload, register_jitable
-from numba.typed import Dict as NumbaDict  # @UnresolvedImport
+from numba.typed import Dict as NumbaDict
 
 from .. import config
 from ..tools.misc import decorator_arguments
@@ -128,12 +128,12 @@ def f():
         "multithreading_threshold": config["numba.multithreading_threshold"],
         "fastmath": config["numba.fastmath"],
         "debug": config["numba.debug"],
-        "using_svml": nb.config.USING_SVML,  # @UndefinedVariable
+        "using_svml": nb.config.USING_SVML,
         "threading_layer": threading_layer,
         "omp_num_threads": os.environ.get("OMP_NUM_THREADS"),
         "mkl_num_threads": os.environ.get("MKL_NUM_THREADS"),
-        "num_threads": nb.config.NUMBA_NUM_THREADS,  # @UndefinedVariable
-        "num_threads_default": nb.config.NUMBA_DEFAULT_NUM_THREADS,  # @UndefinedVariable
+        "num_threads": nb.config.NUMBA_NUM_THREADS,
+        "num_threads_default": nb.config.NUMBA_DEFAULT_NUM_THREADS,
         "cuda_available": cuda_available,
         "roc_available": roc_available,
     }
@@ -203,7 +203,7 @@ def jit(function: TFunc, signature=None, parallel: bool = False, **kwargs) -> TF
     return nb.jit(signature, **kwargs)(function)  # type: ignore
 
 
-if nb.config.DISABLE_JIT:  # @UndefinedVariable
+if nb.config.DISABLE_JIT:
     # dummy function that creates a ctypes pointer
     def address_as_void_pointer(addr):
         """Returns a void pointer from a given memory address.
@@ -321,7 +321,7 @@ def random_seed(seed: int = 0) -> None:
         seed (int): Sets random seed
     """
     np.random.seed(seed)
-    if not nb.config.DISABLE_JIT:  # @UndefinedVariable
+    if not nb.config.DISABLE_JIT:
         _random_seed_compiled(seed)