Merge pull request #525 from ubermag/precommit_updates

Update pre-commits and pytest configuration

.pre-commit-config.yaml

@@ -2,17 +2,14 @@ exclude: 'dev'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-merge-conflict  # checks for files that contain merge conflict strings
   - id: check-toml  # checks toml files for parseable syntax
   - id: debug-statements  # checks for debugger imports and py37+ `breakpoint()` calls in python source
-#  - id: trailing-whitespace   # needs more checks
-#    args: [--markdown-linebreak-ext=md]
-#    exclude: 'discretisedfield/tests/test_sample/.*'
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.11
+  rev: v0.4.4
   hooks:
     # Run the linter.
     - id: ruff

discretisedfield/__init__.py

@@ -1,18 +1,19 @@
 """Finite-difference fields."""
+
 import importlib.metadata
 import pathlib
 
 import matplotlib.pyplot as plt
 import pytest
 
-from . import tools  # noqa: F401
-from .field import Field  # noqa: F401
-from .field_rotator import FieldRotator  # noqa: F401
-from .interact import interact  # noqa: F401
-from .line import Line  # noqa: F401
-from .mesh import Mesh  # noqa: F401
-from .operators import integrate  # noqa: F401
-from .region import Region  # noqa: F401
+from . import tools as tools
+from .field import Field as Field
+from .field_rotator import FieldRotator as FieldRotator
+from .interact import interact as interact
+from .line import Line as Line
+from .mesh import Mesh as Mesh
+from .operators import integrate as integrate
+from .region import Region as Region
 
 # Enable default plotting style.
 plt.style.use(pathlib.Path(__file__).parent / "plotting" / "plotting-style.mplstyle")

discretisedfield/field.py

@@ -601,7 +601,7 @@ def vdim_mapping(self, vdim_mapping):
     def _r_dim_mapping(self):
         """Map dims to vdims."""
         reversed_mapping = {val: key for key, val in self.vdim_mapping.items()}
-        return {dim: reversed_mapping.get(dim, None) for dim in self.mesh.region.dims}
+        return {dim: reversed_mapping.get(dim) for dim in self.mesh.region.dims}
 
     def __abs__(self):
         """Absolute value of the field.
@@ -1647,12 +1647,12 @@ def __truediv__(self, other):
 
         2. Divide vector field by a scalar.
 
-        >>> f1 = df.Field(mesh, nvdim=3, value=(0, 10, 5))
+        >>> f1 = df.Field(mesh, nvdim=3, value=(20, 10, 5))
         >>> res = f1 / 5  # discretisedfield.Field.__mul__ is called
         >>> res.mean()
-        array([0., 2., 1.])
-        >>> (10 / f1).mean()  # division by a vector is not allowed
-        array([inf,  1.,  2.])
+        array([4., 2., 1.])
+        >>> (10 / f1).mean()
+        array([0.5, 1. , 2. ])
 
         .. seealso:: :py:func:`~discretisedfield.Field.__mul__`
 

discretisedfield/io/__init__.py

@@ -5,6 +5,7 @@
 and :py:func:`discretisedfield.Field.fromfile` instead.
 
 """
+
 import json
 import pathlib
 

discretisedfield/io/ovf2vtk.py

@@ -1,4 +1,5 @@
 """OVF to VTK file conversion."""
+
 import argparse
 
 import discretisedfield as df

discretisedfield/mesh.py

@@ -1544,7 +1544,7 @@ def dV(self):
         8.0
 
         """
-        return np.product(self.cell)
+        return np.prod(self.cell)
 
     def scale(self, factor, reference_point=None, inplace=False):
         """Scale the underlying region and all subregions.

discretisedfield/plotting/__init__.py

@@ -1,14 +1,14 @@
 """Matplotlib based plotting."""
-# ruff: noqa: F401
-from discretisedfield.plotting import util
-from discretisedfield.plotting.hv import Hv
-from discretisedfield.plotting.k3d_field import K3dField
-from discretisedfield.plotting.k3d_mesh import K3dMesh
-from discretisedfield.plotting.k3d_region import K3dRegion
-from discretisedfield.plotting.mpl import add_colorwheel
-from discretisedfield.plotting.mpl_field import MplField
-from discretisedfield.plotting.mpl_mesh import MplMesh
-from discretisedfield.plotting.mpl_region import MplRegion
-from discretisedfield.plotting.pyvista_field import PyVistaField
-from discretisedfield.plotting.pyvista_mesh import PyVistaMesh
-from discretisedfield.plotting.pyvista_region import PyVistaRegion
+
+from discretisedfield.plotting import util as util
+from discretisedfield.plotting.hv import Hv as Hv
+from discretisedfield.plotting.k3d_field import K3dField as K3dField
+from discretisedfield.plotting.k3d_mesh import K3dMesh as K3dMesh
+from discretisedfield.plotting.k3d_region import K3dRegion as K3dRegion
+from discretisedfield.plotting.mpl import add_colorwheel as add_colorwheel
+from discretisedfield.plotting.mpl_field import MplField as MplField
+from discretisedfield.plotting.mpl_mesh import MplMesh as MplMesh
+from discretisedfield.plotting.mpl_region import MplRegion as MplRegion
+from discretisedfield.plotting.pyvista_field import PyVistaField as PyVistaField
+from discretisedfield.plotting.pyvista_mesh import PyVistaMesh as PyVistaMesh
+from discretisedfield.plotting.pyvista_region import PyVistaRegion as PyVistaRegion

discretisedfield/plotting/hv.py

@@ -1,4 +1,5 @@
 """Holoviews-based plotting."""
+
 import contextlib
 import copy
 import functools

discretisedfield/plotting/k3d_field.py

@@ -1,4 +1,5 @@
 """K3d based plotting."""
+
 import k3d
 import matplotlib
 import numpy as np

discretisedfield/plotting/mpl.py

@@ -1,4 +1,5 @@
 """Matplotlib-based plotting."""
+
 import abc
 
 import matplotlib.pyplot as plt

discretisedfield/plotting/mpl_field.py

@@ -1,4 +1,5 @@
 """Matplotlib-based plotting."""
+
 import warnings
 
 import matplotlib.pyplot as plt

discretisedfield/tests/test_field.py

@@ -3997,16 +3997,16 @@ def test_pyvista_scalar(test_field):
 
 def test_pyvista_volume(test_field):
     # Default
-    test_field.a.pyvista.volume()
+    test_field.c.pyvista.volume()
 
     # Colormap
-    test_field.a.pyvista.volume(cmap="hsv")
+    test_field.c.pyvista.volume(cmap="hsv")
 
     # Multiplier
-    test_field.a.pyvista.volume(multiplier=1e-6)
+    test_field.c.pyvista.volume(multiplier=1e-6)
 
     # 3D
-    test_field.pyvista.volume(scalars=test_field.vdims[0])
+    test_field.pyvista.volume(scalars=test_field.vdims[2])
 
     # Plotter
     plotter = pv.Plotter()

discretisedfield/tools/__init__.py

@@ -1,13 +1,11 @@
 """Convenience tools"""
-# ruff: noqa: F401
-from .tools import (
-    count_bps,
-    count_large_cell_angle_regions,
-    demag_field,
-    demag_tensor,
-    emergent_magnetic_field,
-    max_neighbouring_cell_angle,
-    neighbouring_cell_angle,
-    topological_charge,
-    topological_charge_density,
-)
+
+from .tools import count_bps as count_bps
+from .tools import count_large_cell_angle_regions as count_large_cell_angle_regions
+from .tools import demag_field as demag_field
+from .tools import demag_tensor as demag_tensor
+from .tools import emergent_magnetic_field as emergent_magnetic_field
+from .tools import max_neighbouring_cell_angle as max_neighbouring_cell_angle
+from .tools import neighbouring_cell_angle as neighbouring_cell_angle
+from .tools import topological_charge as topological_charge
+from .tools import topological_charge_density as topological_charge_density

discretisedfield/tools/tools.py

@@ -273,9 +273,9 @@ def topological_charge(field, /, method="continuous", absolute=False):
 
     q = topological_charge_density(field, method=method)
     if absolute:
-        return float(abs(q).integrate())
+        return abs(q).integrate().item()
     else:
-        return float(q.integrate())
+        return q.integrate().item()
 
 
 def emergent_magnetic_field(field):

discretisedfield/util/__init__.py

@@ -1,2 +1,4 @@
-# ruff: noqa: F401
-from .util import array2tuple, assemble_index, bergluescher_angle, rescale_xarray
+from .util import array2tuple as array2tuple
+from .util import assemble_index as assemble_index
+from .util import bergluescher_angle as bergluescher_angle
+from .util import rescale_xarray as rescale_xarray

pyproject.toml

@@ -68,10 +68,12 @@ repository = "https://github.com/ubermag/discretisedfield"
 [project.scripts]
 ovf2vtk = "discretisedfield.io.ovf2vtk:ovf2vtk"
 
-[tool.ruff]
-ignore-init-module-imports = true  # do not remove unused imports in __init__ and warn instead
+
+[tool.coverage.run]
+omit = ["discretisedfield/tests/*"]
 
 [tool.ruff.lint]
+ignore-init-module-imports = true  # do not remove unused imports in __init__ and warn instead
 select = [
     "B",   # flake8-bugbear
     "E",   # pycodestyle
@@ -97,15 +99,20 @@ ignore = [
 [tool.ruff.lint.isort]
 known-local-folder = ["discretisedfield"]
 
-[tool.ruff.per-file-ignores]
-"*.ipynb" = ["B018", "E501", "F811"]
-# F811: 'redefined-while-unused'; many false positives in notebooks because ipywidgets decorated functions are not recognised
-# E501: line too long
-# B018: "Found useless expression. Either assign it to a variable or remove it."
-
+[tool.ruff.lint.per-file-ignores]
+"*.ipynb" = [
+    "B018",  # "Found useless expression. Either assign it to a variable or remove it."; false positives when using implicit __repr__ in the notebook
+    "E501",  # line too long
+    "F811",  # 'redefined-while-unused'; many false positives in notebooks because ipywidgets decorated functions are not recognised
+]
 
-[tool.coverage.run]
-omit = ["discretisedfield/tests/*"]
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error",
+    "ignore:((.|\n)*)Sentinel is not a public part of the traitlets API((.|\n)*)",  # dependency of k3d
+    "ignore:((.|\n)*)`ipykernel.pylab.backend_inline` is deprecated((.|\n)*)",  # dependency of ipywidgets
+    "ignore:((.|\n)*)Automatic coloring is only supported for 3d fields.((.|\n)*)",  # Our warning
+]
 
 [tool.setuptools.packages.find]
 include = ["discretisedfield*"]

setup.cfg

@@ -1,30 +1,2 @@
-[flake8]
-exclude =
-  .git,
-  __pycache__,
-  build,
-  dev,
-  dist,
-  setup.py
-# black has a longer default line length
-max-line-length = 88
-# D107: missing docstring in __init__
-# E203: withespace before ':', required for black
-# RST210: Inline strong start-string without end-string.  # complains about "**kwargs" in docstrings
-extend-ignore = D107,RST210,E203
-per-file-ignores =
-  # imported but unused
-  __init__.py: F401
-  # ignore missing docstrings in tests
-  test_*.py: D100,D101,D102,D103
-docstring-convention: numpy
-# flake8-rst-docstrings:
-rst-roles =
-  py:class,
-  py:func,
-rst-directives =
-  seealso,
-  plot,
-
 [codespell]
 skip = .*,build/*,dev/*,dist/*

tasks.py

@@ -1,4 +1,5 @@
 """Tasks to release the package."""
+
 import os
 import shutil