utilizing ruff for formatting & linting – #20 (#31)

* initial ruff formating

* lint fastpair

* Update fastpair/test/test_fastpair.py

Co-authored-by: Carson Farmer <carson.farmer@gmail.com>

---------

Co-authored-by: Carson Farmer <carson.farmer@gmail.com>

fastpair/__init__.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 """FastPair: Data-structure for the dynamic closest-pair problem.
 
 Init module for FastPair.

fastpair/base.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 """FastPair: Data-structure for the dynamic closest-pair problem.
 
 This data-structure is based on the observation that the conga line data
@@ -33,27 +30,24 @@
 # Copyright (c) 2002-2015, David Eppstein
 # Licensed under the MIT Licence (http://opensource.org/licenses/MIT).
 
-from __future__ import print_function, division, absolute_import
-from itertools import combinations, cycle
-from operator import itemgetter
 from collections import defaultdict
-import scipy.spatial.distance as dist
+from itertools import combinations, cycle
 
+import scipy.spatial.distance as dist
 
 __all__ = ["FastPair", "dist"]
 
 
-class attrdict(dict):
+class AttrDict(dict):
     """Simple dict with support for accessing elements as attributes."""
 
     def __init__(self, *args, **kwargs):
-        super(attrdict, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.__dict__ = self
 
 
-class FastPair(object):
-    """FastPair 'sketch' class.
-    """
+class FastPair:
+    """FastPair 'sketch' class."""
 
     def __init__(self, min_points=10, dist=dist.euclidean):
         """Initialize an empty FastPair data-structure.
@@ -74,8 +68,8 @@ def __init__(self, min_points=10, dist=dist.euclidean):
         self.min_points = min_points
         self.dist = dist
         self.initialized = False  # Has the data-structure been initialized?
-        self.neighbors = defaultdict(attrdict)  # Dict of neighbor points and dists
-        self.points = list()  # Internal point set; entries may be non-unique
+        self.neighbors = defaultdict(AttrDict)  # Dict of neighbor points and dists
+        self.points = []  # Internal point set; entries may be non-unique
 
     def __add__(self, p):
         """Add a point and find its nearest neighbor.
@@ -99,7 +93,7 @@ def __sub__(self, p):
             # We must update neighbors of points for which `p` had been nearest.
             for q in self.points:
                 if self.neighbors[q].neigh == p:
-                    res = self._find_neighbor(q)
+                    self._find_neighbor(q)
         return self
 
     def __len__(self):
@@ -117,13 +111,13 @@ def __iter__(self):
         return iter(self.points)
 
     def __getitem__(self, item):
-        if not item in self:
-            raise KeyError("{} not found".format(item))
+        if item not in self:
+            raise KeyError(f"{item} not found")
         return self.neighbors[item]
 
     def __setitem__(self, item, value):
-        if not item in self:
-            raise KeyError("{} not found".format(item))
+        if item not in self:
+            raise KeyError(f"{item} not found")
         self._update_point(item, value)
 
     def build(self, points=None):

fastpair/test/test_fastpair.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 """FastPair: Data-structure for the dynamic closest-pair problem.
 
 Testing module for FastPair.
@@ -10,18 +7,17 @@
 # Copyright (c) 2002-2015, David Eppstein
 # Licensed under the MIT Licence (http://opensource.org/licenses/MIT).
 
-from __future__ import print_function, division, absolute_import
-
-from operator import itemgetter
-from types import FunctionType
-from itertools import cycle, combinations, groupby
 import random
-import pytest
-from fastpair import FastPair
+from itertools import combinations, cycle
 from math import isinf, isnan
+from operator import itemgetter
+from types import FunctionType
 
-from scipy import mean, array, unique
 import numpy as np
+import pytest
+from scipy import array, mean
+
+from fastpair import FastPair
 
 
 def normalized_distance(_a, _b):
@@ -63,7 +59,7 @@ def all_close(s, t, tol=1e-8):
     # Ignores inf and nan values...
     return all(
         abs(a - b) < tol
-        for a, b in zip(s, t)
+        for a, b in zip(s, t, strict=True)
         if not isinf(a) and not isinf(b) and not isnan(a) and not isnan(b)
     )
 
@@ -79,7 +75,7 @@ def interact(u, v):
 
 # Setup fixtures
 @pytest.fixture(scope="module")
-def PointSet(n=50, d=10):
+def point_set(n=50, d=10):
     """Return numpy array of shape `n`x`d`."""
     # random.seed(8714)
     return [rand_tuple(d) for _ in range(n)]
@@ -96,15 +92,15 @@ def test_init(self):
         assert len(fp.points) == 0
         assert len(fp.neighbors) == 0
 
-    def test_build(self, PointSet):
-        ps = PointSet
+    def test_build(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         assert len(fp) == len(ps)
         assert len(fp.neighbors) == len(ps)
         assert fp.initialized is True
 
-    def test_add(self, PointSet):
-        ps = PointSet
+    def test_add(self, point_set):
+        ps = point_set
         fp = FastPair()
         for p in ps[:9]:
             fp += p
@@ -114,8 +110,8 @@ def test_add(self, PointSet):
             fp += p
         assert fp.initialized is True
 
-    def test_sub(self, PointSet):
-        ps = PointSet
+    def test_sub(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         start = fp._find_neighbor(ps[-1])
         fp -= ps[-1]
@@ -127,31 +123,31 @@ def test_sub(self, PointSet):
         with pytest.raises(ValueError):
             fp -= rand_tuple(len(ps[0]))
 
-    def test_len(self, PointSet):
-        ps = PointSet
+    def test_len(self, point_set):
+        ps = point_set
         fp = FastPair()
         assert len(fp) == 0
         fp.build(ps)
         assert len(fp) == len(ps)
 
-    def test_contains(self, PointSet):
-        ps = PointSet
+    def test_contains(self, point_set):
+        ps = point_set
         fp = FastPair()
         assert ps[0] not in fp
         fp.build(ps)
         assert ps[0] in fp
 
-    def test_call_and_closest_pair(self, PointSet):
-        ps = PointSet
+    def test_call_and_closest_pair(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         cp = fp.closest_pair()
         bf = fp.closest_pair_brute_force()
         assert fp() == cp
         assert abs(cp[0] - bf[0]) < 1e-8
         assert cp[1] == bf[1]
 
-    def test_all_closest_pairs(self, PointSet):
-        ps = PointSet
+    def test_all_closest_pairs(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         cp = fp.closest_pair()
         bf = fp.closest_pair_brute_force()  # Ordering should be the same
@@ -168,24 +164,24 @@ def test_all_closest_pairs(self, PointSet):
         # Ordering may be different, but both should be in there
         # assert dc[1][0] in cp[1] and dc[1][1] in cp[1]
 
-    def test_find_neighbor_and_sdist(self, PointSet):
-        ps = PointSet
+    def test_find_neighbor_and_sdist(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         rando = rand_tuple(len(ps[0]))
         neigh = fp._find_neighbor(rando)  # Abusing find_neighbor!
         dist = fp.dist(rando, neigh["neigh"])
         assert abs(dist - neigh["dist"]) < 1e-8
         assert len(fp) == len(ps)  # Make sure we didn't add a point...
-        l = [(fp.dist(a, b), b) for a, b in zip(cycle([rando]), ps)]
-        res = min(l, key=itemgetter(0))
+        l_ = [(fp.dist(a, b), b) for a, b in zip(cycle([rando]), ps)]
+        res = min(l_, key=itemgetter(0))
         assert abs(res[0] - neigh["dist"]) < 1e-8
         assert res[1] == neigh["neigh"]
         res = min(fp.sdist(rando), key=itemgetter(0))
         assert abs(neigh["dist"] - res[0]) < 1e-8
         assert neigh["neigh"] == res[1]
 
-    def test_cluster(self, PointSet):
-        ps = PointSet
+    def test_cluster(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         for i in range(len(fp) - 1):
             # Version one
@@ -209,9 +205,9 @@ def test_cluster(self, PointSet):
             assert contains_same(fp.points, ps)
         assert len(fp.points) == len(ps) == 1
 
-    def test_update_point(self, PointSet):
+    def test_update_point(self, point_set):
         # Still failing sometimes...
-        ps = PointSet
+        ps = point_set
         fp = FastPair().build(ps)
         assert len(fp) == len(ps)
         old = ps[0]  # Just grab the first point...
@@ -220,9 +216,9 @@ def test_update_point(self, PointSet):
         assert old not in fp
         assert new in fp
         assert len(fp) == len(ps)  # Size shouldn't change
-        l = [(fp.dist(a, b), b) for a, b in zip(cycle([new]), ps)]
-        res = min(l, key=itemgetter(0))
-        neigh = fp.neighbors[new]
+        l_ = [(fp.dist(a, b), b) for a, b in zip(cycle([new]), ps)]
+        res = min(l_, key=itemgetter(0))  # noqa: F841
+        neigh = fp.neighbors[new]  # noqa: F841
         # assert abs(res[0] - neigh["dist"]) < 1e-8
         # assert res[1] == neigh["neigh"]
 
@@ -267,8 +263,8 @@ def test_call_and_closest_pair_min_points(self, image_array):
         assert abs(cp[0] - bf[0]) < 1e-8
         assert cp[1] == bf[1]
 
-    def test_iter(self, PointSet):
-        ps = PointSet
+    def test_iter(self, point_set):
+        ps = point_set
         fp = FastPair().build(ps)
         assert fp.min_points == 10
         assert isinstance(fp.dist, FunctionType)
@@ -277,23 +273,23 @@ def test_iter(self, PointSet):
         assert fp[ps[0]].neigh in set(ps)
 
         try:
-            myitem = fp[(2, 3, 4)]
+            fp[(2, 3, 4)]
         except KeyError as err:
             print(err)
 
         fp[ps[0]] = fp[ps[0]].neigh
         try:
-            fp[(2, 3, 4)] = fp[ps[0]].neigh
+            assert fp[ps[0]].neigh
         except KeyError as err:
             print(err)
 
-    def test_update_point_less_points(self, PointSet):
-        ps = PointSet
+    def test_update_point_less_points(self, point_set):
+        ps = point_set
         fp = FastPair()
         for p in ps[:9]:
             fp += p
         assert fp.initialized is False
         old = ps[0]  # Just grab the first point...
         new = rand_tuple(len(ps[0]))
-        res = fp._update_point(old, new)
+        fp._update_point(old, new)
         assert len(fp) == 1

pyproject.toml

@@ -46,13 +46,13 @@ tests = [
     "coverage",
     "pytest",
     "pytest-cov",
+    "ruff",
     "setuptools_scm",
 ]
 
 [tool.setuptools.packages.find]
 include = ["fastpair", "fastpair.*"]
 
-
 [tool.coverage.run]
 source = ["./fastpair"]
 
@@ -70,3 +70,12 @@ exclude_lines = [
 
 ignore_errors = true
 omit = ["fastpair/test/*"]
+
+[tool.ruff]
+line-length = 88
+lint.select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
+
+[tool.ruff.lint.per-file-ignores]
+ "*__init__.py" = [
+     "F401",  # imported but unused
+]