Switch linting to ruff (#203)

* use ruff instead of flake8 and others * fine tune ruff to be more similar to what we used so far * enable E721 * ruff (pydocstyle) fixes for previously ignored rules * Fixed typo * update changelog and credits * fixes for B904 * apply B028 * change variable name from e to exception * update pre-commit ruff args so that it exits with 0 on successful fix * Updated doc/development.rst * Fixed ruff order for manual runs --------- Co-authored-by: janbridley <[email protected]>
glotzerlab · Oct 11, 2023 · 6d72539 · 6d72539
1 parent 8cc9183
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -19,52 +19,20 @@ repos:
       - id: check-executables-have-shebangs
       - id: check-json
       - id: check-yaml
-  - repo: https://github.com/asottile/pyupgrade
-    rev: 'v3.8.0'
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.291
     hooks:
-      - id: pyupgrade
-        args:
-          - --py38-plus
-        exclude: '(?:extern/.*)'
-  - repo: https://github.com/PyCQA/isort
-    rev: '5.12.0'
-    hooks:
-      - id: isort
-        exclude: '(?:extern/.*)'
+      - id: ruff
+        args: [ --fix ]
+        types_or: [python, pyi, jupyter]
   - repo: https://github.com/psf/black
     rev: '23.3.0'
     hooks:
       - id: black
         exclude: '(?:extern/.*)'
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: '6.3.0'
-    hooks:
-      - id: pydocstyle
-        exclude: '(?:extern/.*|tests/.*|setup.py|conf.py)'
-        additional_dependencies: [
-          'tomli'
-        ]
-  - repo: https://github.com/PyCQA/flake8
-    rev: '6.0.0'
-    hooks:
-    -   id: flake8
-        additional_dependencies: [
-            'flake8-bugbear==22.1.11',
-            'flake8-rst-docstrings==0.2.5',
-            'pep8==1.7.1',
-            'pep8-naming==0.12.1',
-            'flake8-comprehensions==3.8.0',
-        ]
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.7.0
     hooks:
-      - id: nbqa-pyupgrade
-        args:
-          - --nbqa-mutate
-          - --py36-plus
-      - id: nbqa-isort
-        args:
-          - --nbqa-mutate
       - id: nbqa-black
         args:
           - --nbqa-mutate
diff --git a/ChangeLog.rst b/ChangeLog.rst
@@ -11,6 +11,7 @@ Added
 Changed
 ~~~~~~~
 
+- Pre-commit now uses ruff instead of flake8, pydocstyle, pyupgrade and isort.
 - CI now uses GitHub Actions.
 - Docs ported to furo theme.
 

diff --git a/Credits.rst b/Credits.rst
@@ -118,6 +118,7 @@ Domagoj Fijan
 
 * Rewrote point in polygon check to use NumPy vectorized operations.
 * Rewrote point in polyhedron check to use NumPy vectorized operations.
+* Pre-commit now uses ruff instead of flake8, pydocstyle, pyupgrade and isort.
 * Ported CI to github actions.
 * Ported docs to Furo.
 

diff --git a/coxeter/families/common.py b/coxeter/families/common.py
@@ -35,7 +35,8 @@ def get_shape(cls, n):
             n (int):
                 The number of vertices (greater than or equal to 3).
 
-        Returns:
+        Returns
+        -------
              :class:`~.ConvexPolygon`: The corresponding regular polygon.
         """
         return ConvexPolygon(cls.make_vertices(n))
@@ -48,7 +49,8 @@ def make_vertices(cls, n):
             n (int):
                 An integer greater than or equal to 3.
 
-        Returns:
+        Returns
+        -------
             :math:`(n, 3)` :class:`numpy.ndarray` of float: The vertices of the polygon.
         """
         if n < 3:

diff --git a/coxeter/families/plane_shape_families.py b/coxeter/families/plane_shape_families.py
@@ -42,7 +42,8 @@ class TruncationPlaneShapeFamily(ShapeFamily):
     def get_planes(cls):
         """Get the set of planes used to truncate the shape.
 
-        Returns:
+        Returns
+        -------
             (:math:`N_{planes}`, 3) :class:`numpy.ndarray` of float:
                 The planes defining this family
         """
@@ -58,7 +59,8 @@ def get_plane_types(cls):
         * type 1 corresponds to the parameter b.
         * type 2 corresponds to the parameter c.
 
-        Returns:
+        Returns
+        -------
             (:math:`N_{planes}`, ) :class:`numpy.ndarray` of int:
                 The plane types.
         """
@@ -73,7 +75,8 @@ def make_vertices(cls, a, b, c):
             b (float): The b parameter.
             c (float): The c parameter.
 
-        Returns:
+        Returns
+        -------
             (:math:`N_{vertices}`, 3) :class:`numpy.ndarray` of float:
                 The vertices of the shape generated by the provided parameters.
         """
@@ -174,7 +177,8 @@ def get_shape(cls, a, c):
             c (float):
                 The parameter :math:`c \in [1, 3]`.
 
-        Returns:
+        Returns
+        -------
             :class:`~coxeter.shapes.ConvexPolyhedron`:
                 The desired shape.
         """
@@ -246,7 +250,8 @@ def get_shape(cls, a, c):
             c (float):
                 The parameter :math:`c \in [2, 3]`.
 
-        Returns:
+        Returns
+        -------
             :class:`~coxeter.shapes.ConvexPolyhedron`:
                 The desired shape.
         """
@@ -426,7 +431,8 @@ def get_shape(cls, a, c):
             c (float):
                 The parameter :math:`c \in [S^2, 3]`.
 
-        Returns:
+        Returns
+        -------
             :class:`~coxeter.shapes.ConvexPolyhedron`:
                 The desired shape.
         """
@@ -463,7 +469,8 @@ def get_shape(cls, truncation):
             truncation (float):
                 The parameter :math:`truncation \in [0, 1]`.
 
-        Returns:
+        Returns
+        -------
             :class:`~coxeter.shapes.ConvexPolyhedron`:
                 The desired truncated tetrahedron.
         """

diff --git a/coxeter/families/tabulated_shape_family.py b/coxeter/families/tabulated_shape_family.py
@@ -48,7 +48,8 @@ def from_mapping(cls, mapping, classname=None, docstring=None):
             docstring (str, optional):
                 The docstring to apply to the class.
 
-        Returns:
+        Returns
+        -------
             A subclass of this one associated with the the provided data.
         """
 
@@ -79,7 +80,8 @@ def from_json_file(cls, filename, *args, **kwargs):
             \*\*kwargs:
                 Passed on to :meth:`~.from_mapping`.
 
-        Returns:
+        Returns
+        -------
             A subclass of this one associated with the the provided data.
         """
         with open(filename) as f:
@@ -108,7 +110,8 @@ def get_shape(cls, name):
             name (str):
                 The key of the desired shape in the data dict.
 
-        Returns:
+        Returns
+        -------
             :class:`~coxeter.shapes.Shape`: The requested shape.
         """
         return from_gsd_type_shapes(cls.data[name])
diff --git a/coxeter/shape_getters.py b/coxeter/shape_getters.py
@@ -1,7 +1,7 @@
 # Copyright (c) 2021 The Regents of the University of Michigan
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
-"""This module defines various convenience functions for generating shapes.
+"""Module for defining various convenience functions for shape generation.
 
 The methods here provide routes for generating instances of
 :class:`~coxeter.shapes.Shape` based on certain pre-specified mappings.
@@ -42,7 +42,8 @@ def from_gsd_type_shapes(params, dimensions=3):  # noqa: C901
             instead of a :class:`~.shapes.Sphere` or
             :class:`~.shapes.Ellipsoid` (Default value: 3).
 
-    Returns:
+    Returns
+    -------
         :class:`~coxeter.shapes.Shape`:
             The desired shape.
     """

diff --git a/coxeter/shapes/base_classes.py b/coxeter/shapes/base_classes.py
@@ -57,7 +57,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the shape.
         """
@@ -117,7 +118,8 @@ def distance_to_surface(self, angles):
                 Angles between :math:`0` and :math:`2 \pi` over which to
                 calculate the distances. :math:`d` is the number of dimensions.
 
-        Returns:
+        Returns
+        -------
             :math:`(N,)` :class:`numpy.ndarray`:
                 An array of distances from the center of the shape to its surface
                 at each of the given angles.
@@ -164,11 +166,13 @@ def to_plato_scene(self, backend="matplotlib", scene=None, scene_kwargs=None):
                 (Default value: None). Only used if ``scene`` is not provided
                 or None.
 
-        Returns:
+        Returns
+        -------
             :class:`plato.draw.Scene`:
                 A scene containing this shape.
 
-        Raises:
+        Raises
+        ------
             NotImplementedError:
                 If no plato primitive corresponds to this coxeter shape class.
             AttributeError:
@@ -180,10 +184,10 @@ def to_plato_scene(self, backend="matplotlib", scene=None, scene_kwargs=None):
                 import importlib
 
                 backend = importlib.import_module(f"plato.draw.{backend}")
-            except ImportError:
+            except ImportError as exception:
                 raise ImportError(
                     f"Backend plato.draw.{backend} could not be imported."
-                )
+                ) from exception
             if scene_kwargs is None:
                 scene_kwargs = {}
             prim = self._plato_primitive(backend)

diff --git a/coxeter/shapes/circle.py b/coxeter/shapes/circle.py
@@ -166,7 +166,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the
                 circle.

diff --git a/coxeter/shapes/convex_polygon.py b/coxeter/shapes/convex_polygon.py
@@ -25,7 +25,8 @@ def _is_convex(vertices, normal):
         normal (:math:`(3, )` :class:`numpy.ndarray`):
             The normal to the vertices.
 
-    Returns:
+    Returns
+    -------
         bool: ``True`` if ``vertices`` define a convex polygon.
 
     """
@@ -168,6 +169,7 @@ def incircle_from_center(self):
             "The incircle_from_center property is deprecated, use "
             "maximal_centered_bounded_circle instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.maximal_centered_bounded_circle
 

diff --git a/coxeter/shapes/convex_polyhedron.py b/coxeter/shapes/convex_polyhedron.py
@@ -143,7 +143,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the
                 polyhedron.
@@ -157,6 +158,7 @@ def insphere_from_center(self):
             "The insphere_from_center property is deprecated, use "
             "maximal_centered_bounded_sphere instead",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.maximal_centered_bounded_sphere
 
@@ -172,6 +174,7 @@ def circumsphere_from_center(self):
             "The circumsphere_from_center property is deprecated, use "
             "minimal_centered_bounding_sphere instead",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.minimal_centered_bounding_sphere
 

diff --git a/coxeter/shapes/convex_spheropolyhedron.py b/coxeter/shapes/convex_spheropolyhedron.py
@@ -190,7 +190,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the
                 spheropolyhedron.

diff --git a/coxeter/shapes/ellipse.py b/coxeter/shapes/ellipse.py
@@ -242,7 +242,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the
                 ellipsoid.

diff --git a/coxeter/shapes/ellipsoid.py b/coxeter/shapes/ellipsoid.py
@@ -184,7 +184,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the
                 ellipsoid.

diff --git a/coxeter/shapes/polygon.py b/coxeter/shapes/polygon.py
@@ -39,7 +39,8 @@ def _align_points_by_normal(normal, points):
         points (:math:`(N, 3)` :class:`numpy.ndarray`):
             The points that will be rotated and returned.
 
-    Returns:
+    Returns
+    -------
        :math:`(N, 3)` :class:`numpy.ndarray`: The rotated points.
     """
     # Since we are considering just a single vector, to avoid getting a pure
@@ -465,6 +466,7 @@ def bounding_circle(self):
             "The bounding_circle property is deprecated, use "
             "minimal_bounding_circle instead",
             DeprecationWarning,
+            stacklevel=2,
         )
 
         return self.minimal_bounding_circle
@@ -516,7 +518,8 @@ def circumcircle(self):
         of linear equations defined by this constraint, and the circumcircle
         only exists if the resulting solution has no residual.
 
-        Raises:
+        Raises
+        ------
             RuntimeError: If no circumcircle exists for this polygon.
         """
         # The circumsphere is defined by center C and radius r. For vertex i
@@ -664,7 +667,7 @@ def compute_form_factor_amplitude(self, q, density=1.0):  # noqa: D102
         return form_factor
 
     def is_inside(self, points):
-        r"""Simple point-in-polygon algorithm based on winding number.
+        r"""Implement a simple point-in-polygon algorithm based on winding number.
 
         The code in this function is based on implementation in :cite:`Dickinson2019`
         which is licensed under the BSD-3 license.
@@ -703,7 +706,8 @@ def is_inside(self, points):
             points (:math:`(N, 3)` or :math:`(N, 2)` :class:`numpy.ndarray`):
                 The points to test.
 
-        Returns:
+        Returns
+        -------
             :math:`(N, )` :class:`numpy.ndarray`:
                 Boolean array indicating which points are contained in the
                 polyhedron.
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ Added @@
     Changed
     ~~~~~~~
+    - Pre-commit now uses ruff instead of flake8, pydocstyle, pyupgrade and isort.
     - CI now uses GitHub Actions.
     - Docs ported to furo theme.
@@ Expand Down @@