Reup ruff linting & formatting [2025-07] (#795)

Author: jGaboardi

.pre-commit-config.yaml

@@ -1,9 +1,9 @@
 files: "libpysal\/|docs\/"
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.9"
+    rev: "v0.12.2"
     hooks:
-      - id: ruff
+      - id: ruff-check
       - id: ruff-format
 
 ci:

docs/user-guide/graph/matching-graph.ipynb

@@ -111,7 +111,7 @@
     "f, ax = plt.subplots(1, 3)\n",
     "for i, g in enumerate((g1, g2, g3)):\n",
     "    g.plot(gdf, ax=ax[i])\n",
-    "    ax[i].set_title(f\"k = {i+1}\")"
+    "    ax[i].set_title(f\"k = {i + 1}\")"
    ]
   },
   {

docs/user-guide/weights/voronoi.ipynb

@@ -316,7 +316,7 @@
     "points_df.plot(ax=ax, color=\"red\")\n",
     "plt.xlim(minx, maxx)\n",
     "plt.ylim(miny, maxy)\n",
-    "plt.title(\"buffer: %f, n: %d\" % (r, n_points))\n",
+    "plt.title(f\"buffer: {r}, n: {n_points}\")\n",
     "plt.show()"
    ]
   },
@@ -467,7 +467,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.2"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,

libpysal/cg/alpha_shapes.py

@@ -557,7 +557,7 @@ def alpha_shape_auto(
     geoms_prev = _alpha_geoms((1 / radii.max()) - EPS, triangles, radii, xys)
     points = shapely.points(xys)
     if verbose:
-        print("Step set to %i" % step)
+        print(f"Step set to {step}")
     for i in range(0, len(radii), step):
         radi = radii[i]
         alpha = (1 / radi) - EPS

libpysal/cg/rtree.py

@@ -1197,7 +1197,7 @@ def k_means_cluster(root, k, nodes):
         for c in clusters:
             if len(c) == 0:
                 print("Error....")
-                print("Nodes: %d, centers: %s." % (len(ns), repr(cluster_centers)))
+                print(f"Nodes: {len(ns)}, centers: {repr(cluster_centers)}.")
 
             assert len(c) > 0
 

libpysal/cg/segmentLocator.py

@@ -367,11 +367,11 @@ def brute_check(segments, qpoints):  # noqa: ARG001
     t0 = time.time()
     g2 = BruteSegmentLocator(segs)
     t1 = time.time()
-    print("Created Brute in %0.4f seconds" % (t1 - t0))
+    print(f"Created Brute in {t1 - t0:0.4f} seconds")
     t2 = time.time()
     q = list(map(g2.nearest, qpoints))
     t3 = time.time()
-    print("Brute Found %d matches in %0.4f seconds" % (len(qpoints), t3 - t2))
+    print(f"Brute Found {len(qpoints)} matches in {t3 - t2:0.4f} seconds")
     print("Total Brute Time:", t3 - t0)
     print()
     return q
@@ -383,8 +383,8 @@ def grid_check(bins, segments, qpoints, visualize=False):
     t1 = time.time()
     g.grid.kd  # noqa: B018
     t2 = time.time()
-    print("Created Grid in %0.4f seconds" % (t1 - t0))
-    print("Created KDTree in %0.4f seconds" % (t2 - t1))
+    print(f"Created Grid in {t1 - t0:0.4f} seconds")
+    print(f"Created KDTree in {t2 - t1:0.4f} seconds")
     if visualize:
         pylab.matshow(
             g.grid.mask, origin="lower", extent=g.grid.x_range + g.grid.y_range
@@ -393,7 +393,7 @@ def grid_check(bins, segments, qpoints, visualize=False):
     t2 = time.time()
     list(map(g.nearest, qpoints))
     t3 = time.time()
-    print("Grid Found %d matches in %0.4f seconds" % (len(qpoints), t3 - t2))
+    print(f"Grid Found {len(qpoints)} matches in {t3 - t2:0.4f} seconds")
     print("Total Grid Time:", t3 - t0)
     qps = len(qpoints) / (t3 - t2)
     print("q/s:", qps)

libpysal/examples/remotes.py

@@ -20,7 +20,7 @@
     },
     "Atlanta": {
         "download_url": (
-            "https://geodacenter.github.io/data-and-lab/" "/data/atlanta_hom.zip"
+            "https://geodacenter.github.io/data-and-lab//data/atlanta_hom.zip"
         ),
         "explain_url": "https://geodacenter.github.io/data-and-lab//atlanta_old/",
         "n": "90",
@@ -197,8 +197,7 @@
             "https://geodacenter.github.io/data-and-lab//data/income_diversity.zip"
         ),
         "explain_url": (
-            "https://geodacenter.github.io/data-and-lab/"
-            "/co_income_diversity_variables/"
+            "https://geodacenter.github.io/data-and-lab//co_income_diversity_variables/"
         ),
         "n": " 3,984",
         "k": " 64",
@@ -507,15 +506,13 @@
     },
     "SanFran Crime": {
         "download_url": (
-            "https://geodacenter.github.io/data-and-lab/"
-            "/data/SFCrime_July_Dec2012.zip"
+            "https://geodacenter.github.io/data-and-lab//data/SFCrime_July_Dec2012.zip"
         ),
         "explain_url": "https://geodacenter.github.io/data-and-lab//SFcrimes_vars/",
         "n": " 3,384",
         "k": " 13",
         "description": (
-            " July-Dec 2012 crime incidents in San Francisco "
-            "(points + area) - for CAST"
+            " July-Dec 2012 crime incidents in San Francisco (points + area) - for CAST"
         ),
     },
     "Savannah1": {

libpysal/graph/_kernel.py

@@ -140,9 +140,9 @@ def _kernel(
             coordinates, ids=ids, valid_geometry_types=_VALID_GEOMETRY_TYPES
         )
     else:
-        assert (
-            coordinates.shape[0] == coordinates.shape[1]
-        ), "coordinates should represent a distance matrix if metric='precomputed'"
+        assert coordinates.shape[0] == coordinates.shape[1], (
+            "coordinates should represent a distance matrix if metric='precomputed'"
+        )
         if ids is None:
             ids = numpy.arange(coordinates.shape[0])
 

libpysal/graph/_summary.py

@@ -227,40 +227,40 @@ def __init__(self, graph, asymmetries=False):
     def __repr__(self):
         n_asymmetries = f"{self.n_asymmetries:>12.0f}" if self.asymmetries else "NA"
         return f"""Graph Summary Statistics
-{'='*24}
+{"=" * 24}
 Graph indexed by:
  {self._graph._get_ids_repr(57)}
-{'='*62}
+{"=" * 62}
 {"Number of nodes:":<50}{self.n_nodes:>12.0f}
 {"Number of edges:":<50}{self.n_edges:>12.0f}
 {"Number of connected components:":<50}{self.n_components:>12.0f}
 {"Number of isolates:":<50}{self.n_isolates:12.0f}
 {"Number of non-zero edges:":<50}{self.nonzero:>12.0f}
 {"Percentage of non-zero edges:":<50}{self.pct_nonzero:>11.2f}%
 {"Number of asymmetries:":<50}{n_asymmetries}
-{'-'*62}
+{"-" * 62}
 Cardinalities
-{'='*62}
+{"=" * 62}
 {"Mean:":<20}{self.cardinalities_mean:>9.0f}    {"25%:":<20}{self.cardinalities_25:>9.0f}
 {"Standard deviation:":<20}{self.cardinalities_std:>9.0f}    {"50%:":<20}{self.cardinalities_50:>9.0f}
 {"Min:":<20}{self.cardinalities_min:>9.0f}    {"75%:":<20}{self.cardinalities_75:>9.0f}
 {"Max:":<20}{self.cardinalities_max:>9.0f}
-{'-'*62}
+{"-" * 62}
 Weights
-{'='*62}
+{"=" * 62}
 {"Mean:":<20}{self.weights_mean:>9.0f}    {"25%:":<20}{self.weights_25:>9.0f}
 {"Standard deviation:":<20}{self.weights_std:>9.0f}    {"50%:":<20}{self.weights_50:>9.0f}
 {"Min:":<20}{self.weights_min:>9.0f}    {"75%:":<20}{self.weights_75:>9.0f}
 {"Max:":<20}{self.weights_max:>9.0f}
-{'-'*62}
+{"-" * 62}
 Sum of weights
-{'='*62}
+{"=" * 62}
 {"S0:":<50}{self.s0:>12.0f}
 {"S1:":<50}{self.s1:>12.0f}
 {"S2:":<50}{self.s2:>12.0f}
-{'-'*62}
+{"-" * 62}
 Traces
-{'='*62}
+{"=" * 62}
 {"GG:":<50}{self.trace_g2:>12.0f}
 {"G'G:":<50}{self.trace_gtg:>12.0f}
 {"G'G + GG:":<50}{self.trace_gtg_gg:>12.0f}

libpysal/graph/tests/test_base.py

@@ -139,8 +139,7 @@ def test_init(self):
 
     def test___repr__(self):
         expected = (
-            "<Graph of 10 nodes and 25 nonzero edges indexed by\n"
-            " [0, 1, 2, 3, 4, ...]>"
+            "<Graph of 10 nodes and 25 nonzero edges indexed by\n [0, 1, 2, 3, 4, ...]>"
         )
         assert repr(self.g_int) == expected
 
@@ -371,9 +370,9 @@ def test_from_sparse(self):
             ],
             np.ones(10),
         )
-        assert (
-            g == expected
-        ), "sparse csr nybb with ids does not match arrays constructor"
+        assert g == expected, (
+            "sparse csr nybb with ids does not match arrays constructor"
+        )
         np.testing.assert_array_equal(g.sparse.todense(), sp.todense())
 
         with pytest.raises(ValueError, match="The length of ids "):