Apply flake8+pycodestyles autofixes (#342)

Author: Avasam

pyproject.toml

@@ -27,24 +27,33 @@ line-length = 130
 target-version = "py39"
 
 [tool.ruff.lint]
-# TODO: Use extend-select instead to get base E and F rules that don't conflict with the formatter
-select = [
+extend-select = [
     "FA", # flake8-future-annotations
     "I", # isort
     "PYI", # flake8-pyi
     "UP", # pyupgrade
+    "W", # pycodestyle Warning
 ]
 ignore = [
     ###
     # Rules we don't want or don't agree with
     ###
 
+    # Used for direct, non-subclass type comparison, for example: `type(val) is str`
+    # see https://github.com/astral-sh/ruff/issues/6465
+    "E721", # Do not compare types, use `isinstance()`
+
     # Typeshed doesn't want complex or non-literal defaults, or long strings, for maintenance and testing reasons.
     # This doesn't affect us, let's have more complete stubs.
     "PYI011",
     "PYI014",
     "PYI053",
 
+    # TODO: Fixing these would change which symbols are even visible for Pylance.
+    # Which may negatively affect users, especially if the symbol wasn't meant to be re-exported.
+    # Manually evaluate each violation.
+    "F401",
+
     # TODO: Investigate and fix or configure
     "PYI001",
     "PYI002",
@@ -55,8 +64,18 @@ ignore = [
     "PYI051", # Request for autofix: https://github.com/astral-sh/ruff/issues/14185
     "PYI052",
 ]
-
 [tool.ruff.lint.per-file-ignores]
+"*.pyi" = [
+    ###
+    # Rules that are out of the control of stub authors:
+    ###
+    "E743", # Ambiguous function name; stubs must follow implementation
+    "F403", # `from . import *` used; unable to detect undefined names
+    # Stubs can sometimes re-export entire modules.
+    # Issues with using a star-imported name will be caught by type-checkers.
+    "F405", # may be undefined, or defined from star imports
+]
+
 # We keep docstrings in sklearn
 "stubs/sklearn/**" = ["PYI021"]
 

stubs/matplotlib/pyplot.pyi

@@ -11,7 +11,6 @@ import numpy as np
 from matplotlib import rcParams as rcParams, style as style
 from matplotlib.contour import QuadContourSet
 
-from . import rcParams
 from ._typing import *
 from .artist import Artist
 from .axes import Axes as Axes
@@ -780,7 +779,7 @@ def tick_params(axis: Literal["x", "y", "both"] = ..., **kwargs): ...
 def ticklabel_format(
     *,
     axis: Literal["x", "y", "both"] = ...,
-    style: Literal["sci", "scientific", "plain"] = ...,
+    style: Literal["sci", "scientific", "plain"] = ...,  # noqa: F811
     scilimits=...,
     useOffset: bool | float = ...,
     useLocale: bool = ...,

stubs/matplotlib/widgets.pyi

@@ -9,9 +9,6 @@ import numpy as np
 from matplotlib.axes._axes import Axes
 from matplotlib.backend_bases import DrawEvent, Event, FigureCanvasBase, KeyEvent, MouseButton, MouseEvent
 from matplotlib.figure import Figure
-from matplotlib.lines import Line2D
-from matplotlib.patches import Ellipse, Rectangle
-from matplotlib.transforms import Affine2D
 from numpy import float64, ndarray
 from numpy.typing import ArrayLike
 from PIL.Image import Image

stubs/networkx/algorithms/community/__init__.pyi

@@ -1,22 +1,11 @@
-from .asyn_fluid import asyn_fluidc as asyn_fluidc
-from .centrality import girvan_newman as girvan_newman
-from .community_utils import is_partition as is_partition
-from .kclique import k_clique_communities as k_clique_communities
-from .kernighan_lin import kernighan_lin_bisection as kernighan_lin_bisection
-from .label_propagation import (
-    asyn_lpa_communities as asyn_lpa_communities,
-    asyn_lpa_communities as label_propagation_communities,
-    label_propagation_communities as label_propagation_communities,
-)
-from .louvain import louvain_communities as louvain_communities, louvain_partitions as louvain_partitions
-from .lukes import lukes_partitioning as lukes_partitioning
-from .modularity_max import (
-    greedy_modularity_communities as greedy_modularity_communities,
-    naive_greedy_modularity_communities as naive_greedy_modularity_communities,
-)
-from .quality import (
-    coverage as coverage,
-    modularity as modularity,
-    partition_quality as partition_quality,
-    performance as performance,
-)
+from networkx.algorithms.community.asyn_fluid import *
+from networkx.algorithms.community.centrality import *
+from networkx.algorithms.community.community_utils import *
+from networkx.algorithms.community.divisive import *
+from networkx.algorithms.community.kclique import *
+from networkx.algorithms.community.kernighan_lin import *
+from networkx.algorithms.community.label_propagation import *
+from networkx.algorithms.community.louvain import *
+from networkx.algorithms.community.lukes import *
+from networkx.algorithms.community.modularity_max import *
+from networkx.algorithms.community.quality import *

stubs/networkx/algorithms/connectivity/connectivity.pyi

@@ -6,11 +6,10 @@ from operator import itemgetter
 # connectivity algorithms.
 from ...algorithms.flow import boykov_kolmogorov, build_residual_network, dinitz, edmonds_karp, shortest_augmenting_path
 from ...classes.graph import Graph
+from .utils import build_auxiliary_edge_connectivity, build_auxiliary_node_connectivity
 
 default_flow_func = ...
 
-from .utils import build_auxiliary_edge_connectivity, build_auxiliary_node_connectivity
-
 __all__ = [
     "average_node_connectivity",
     "local_node_connectivity",

stubs/networkx/algorithms/connectivity/cuts.pyi

@@ -4,11 +4,10 @@ import itertools
 # cut algorithms.
 from ...algorithms.flow import build_residual_network, edmonds_karp
 from ...classes.graph import Graph
+from .utils import build_auxiliary_edge_connectivity, build_auxiliary_node_connectivity
 
 default_flow_func = ...
 
-from .utils import build_auxiliary_edge_connectivity, build_auxiliary_node_connectivity
-
 __all__ = [
     "minimum_st_node_cut",
     "minimum_node_cut",

stubs/networkx/algorithms/connectivity/disjoint_paths.pyi

@@ -1,15 +1,16 @@
 # Define the default maximum flow function to use for the undelying
 # maximum flow computations
+from itertools import filterfalse as _filterfalse
+
 from ...algorithms.flow import edmonds_karp, preflow_push, shortest_augmenting_path
 from ...classes.graph import Graph
 from ...exception import NetworkXNoPath
 
-default_flow_func = ...
-from itertools import filterfalse as _filterfalse
-
 # Functions to build auxiliary data structures.
 from .utils import build_auxiliary_edge_connectivity, build_auxiliary_node_connectivity
 
+default_flow_func = ...
+
 __all__ = ["edge_disjoint_paths", "node_disjoint_paths"]
 
 def edge_disjoint_paths(

stubs/networkx/algorithms/tree/branchings.pyi

@@ -24,7 +24,6 @@ from operator import itemgetter
 from queue import PriorityQueue
 from typing import Literal
 
-from ...algorithms.tree.branchings import ArborescenceIterator
 from ...classes.digraph import DiGraph
 from ...classes.graph import Graph
 from ...classes.multidigraph import MultiDiGraph

stubs/networkx/algorithms/tree/decomposition.pyi

@@ -3,7 +3,6 @@ from itertools import combinations
 from networkx import Graph
 
 from ...algorithms import chordal_graph_cliques, complete_to_chordal_graph, moral
-from ...classes.graph import Graph
 from ...utils import not_implemented_for
 
 __all__ = ["junction_tree"]

stubs/networkx/algorithms/tree/mst.pyi

@@ -6,7 +6,6 @@ from math import isnan
 from operator import itemgetter
 from queue import PriorityQueue
 
-from ...algorithms.tree.mst import SpanningTreeIterator
 from ...classes.graph import Graph
 from ...utils import UnionFind, not_implemented_for, py_random_state