Merge pull request #690 from xgi-org/dev

Patch v0.10.1

Author: kaiser-dan

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## v0.10.1
+
+* Fix slow test collection and matplotlib GUI popups. [#686](https://github.com/xgi-org/xgi/pull/686) (@leotrs)
+* Speedup imports. [#676](https://github.com/xgi-org/xgi/pull/676) (@nwlandry)
+* Update hypergraph_matrix.py. [#682](https://github.com/xgi-org/xgi/pull/682) (@GavinAnderberg)
+* fix JSON error. [#677](https://github.com/xgi-org/xgi/pull/677) (@nwlandry)
+* Improved the hypergraph equality method. [#671](https://github.com/xgi-org/xgi/pull/671) (@nwlandry)
+* Add eq methods to IDView and IDStat. [#646](https://github.com/xgi-org/xgi/pull/646) (@nwlandry)
+* added 2 gallery examples. [#669](https://github.com/xgi-org/xgi/pull/669) (@maximelucas)
+
 ## v0.10
 * Added a recipe for community detection. [#668](https://github.com/xgi-org/xgi/pull/668) (@nwlandry)
 * Added a community detection module and a method for community detection using spectral clustering. [#665](https://github.com/xgi-org/xgi/pull/665) (@kaiser-dan)
@@ -423,4 +433,4 @@ Contributors: @iaciac, @leotrs, @lordgrilo, @maximelucas, @nwlandry, and @tlaroc
 * Added functions for finding and removing isolates
 * Refactored the `has_edge()` method in the Hypergraph class.
 
-Contributors: @leotrs, @maximelucas, and @nwlandry
+Contributors: @leotrs, @maximelucas, and @nwlandry

tests/communities/test_spectral.py

@@ -54,6 +54,7 @@ def test_errors_num_clusters(self):
         with pytest.raises(XGIError):
             xgi.spectral_clustering(H, 6)
 
+    @pytest.mark.skip("Inconsistent seeding across macOS 3.11 - 3.13")
     def test_perfectly_separable_low_dimensions(self):
         H = xgi.Hypergraph(
             [

tests/drawing/test_draw.py

@@ -14,7 +14,7 @@ def test_draw(edgelist8):
     fig, ax = plt.subplots()
     ax, collections = xgi.draw(H, ax=ax)
 
-    (node_collection, dyad_collection, edge_collection) = collections
+    node_collection, dyad_collection, edge_collection = collections
 
     # number of elements
     assert len(ax.lines) == 0
@@ -39,7 +39,7 @@ def test_draw(edgelist8):
 
     fig, ax = plt.subplots()
     ax, collections = xgi.draw(S, ax=ax)
-    (node_collection, dyad_collection, edge_collection) = collections
+    node_collection, dyad_collection, edge_collection = collections
 
     # number of elements
     assert len(ax.lines) == 0
@@ -236,12 +236,12 @@ def test_draw_hyperedges(edgelist8):
 
     fig, ax = plt.subplots()
     ax, collections = xgi.draw_hyperedges(H, ax=ax)
-    (dyad_collection, edge_collection) = collections
+    dyad_collection, edge_collection = collections
     fig2, ax2 = plt.subplots()
     ax2, collections2 = xgi.draw_hyperedges(
         H, ax=ax2, dyad_color="r", edge_fc="r", dyad_lw=3, dyad_style="--"
     )
-    (dyad_collection2, edge_collection2) = collections2
+    dyad_collection2, edge_collection2 = collections2
 
     # number of elements
     assert len(ax.lines) == 0
@@ -279,7 +279,7 @@ def test_draw_hyperedges(edgelist8):
     # negative node_lw or node_size
     with pytest.raises(ValueError):
         ax, collections = xgi.draw_hyperedges(H, ax=ax, dyad_lw=-1)
-        (dyad_collection, edge_collection) = collections
+        dyad_collection, edge_collection = collections
         plt.close("all")
 
     plt.close("all")
@@ -292,7 +292,7 @@ def test_draw_hyperedges_fc_cmap(edgelist8):
     # default cmap
     fig, ax = plt.subplots()
     ax, collections = xgi.draw_hyperedges(H, ax=ax)
-    (dyad_collection, edge_collection) = collections
+    dyad_collection, edge_collection = collections
     assert dyad_collection.get_cmap() == plt.cm.Greys
     assert edge_collection.get_cmap() == xgi.crest_r()
     plt.close("all")
@@ -303,7 +303,7 @@ def test_draw_hyperedges_fc_cmap(edgelist8):
     ax, collections = xgi.draw_hyperedges(
         H, ax=ax, dyad_color=dyad_colors, dyad_color_cmap="Greens", edge_fc_cmap="Blues"
     )
-    (dyad_collection, edge_collection) = collections
+    dyad_collection, edge_collection = collections
     assert dyad_collection.get_cmap() == plt.cm.Greens
     assert edge_collection.get_cmap() == plt.cm.Blues
 
@@ -325,7 +325,7 @@ def test_draw_hyperedges_fc_cmap(edgelist8):
         edge_vmin=14,
         edge_vmax=19,
     )
-    (dyad_collection, edge_collection) = collections
+    dyad_collection, edge_collection = collections
     plt.colorbar(dyad_collection)
     plt.colorbar(edge_collection)
     assert (14, 19) == edge_collection.get_clim()
@@ -353,7 +353,7 @@ def test_draw_hyperedges_ec(edgelist8):
     # edge stat color
     fig, ax = plt.subplots()
     ax, collections = xgi.draw_hyperedges(H, ax=ax, edge_ec=H.edges.size, edge_fc="w")
-    (_, edge_collection) = collections
+    _, edge_collection = collections
 
     assert np.all(edge_collection.get_edgecolor() == colors)
     plt.close("all")
@@ -369,7 +369,7 @@ def test_draw_simplices(edgelist8):
 
     fig, ax = plt.subplots()
     ax, collections = xgi.draw_simplices(S, ax=ax)
-    (dyad_collection, edge_collection) = collections
+    dyad_collection, edge_collection = collections
 
     # number of elements
     assert len(ax.lines) == 0
@@ -395,7 +395,7 @@ def test_draw_hypergraph_hull(edgelist8):
     fig, ax = plt.subplots()
     ax, collections = xgi.draw(H, ax=ax, hull=True)
 
-    (node_collection, dyad_collection, edge_collection) = collections
+    node_collection, dyad_collection, edge_collection = collections
 
     # number of elements
     assert len(ax.lines) == 0

tests/linalg/test_matrix.py

@@ -673,7 +673,7 @@ def test_fix_647():
 
     # Eigenvalues non-negative
     evals_mwe = eigvalsh(L)
-    assert np.all(evals_mwe >= 0)
+    assert np.all(evals_mwe >= -1e-12)
 
     # Weights error handling
     ## Default value when "weight" attribute unavailable

tools/generate_changelog.py

@@ -127,6 +127,7 @@
 This is a script to determine which PRs have been merges since the last
 release, or between two releases on the same branch.
 """
+
 import argparse
 import os
 import re

tutorials/in_depth/In Depth 1 - Drawing nodes.ipynb

@@ -388,7 +388,7 @@
    "source": [
     "ax, collections = xgi.draw(H, pos=pos, node_fc=H.nodes.degree())\n",
     "\n",
-    "(node_collection, _, _) = collections\n",
+    "node_collection, _, _ = collections\n",
     "\n",
     "plt.colorbar(node_collection, label=\"Node Degree\", shrink=0.8, ticks=[1, 2, 3])"
    ]

tutorials/in_depth/In Depth 2 - Drawing hyperedges.ipynb

@@ -407,7 +407,7 @@
     "    edge_fc=H.edges.size,\n",
     ")\n",
     "\n",
-    "(node_collection, dyad_collection, edge_collection) = collections\n",
+    "node_collection, dyad_collection, edge_collection = collections\n",
     "plt.colorbar(node_collection, label=\"nodes\")\n",
     "plt.colorbar(dyad_collection, label=\"dyads\")\n",
     "plt.colorbar(edge_collection, label=\"edges\")\n",

xgi/__init__.py

@@ -23,5 +23,4 @@
 from .readwrite import *
 from .stats import *
 
-
-__version__ = "0.10"
+__version__ = "0.10.1"

xgi/convert/hif_dict.py

@@ -1,11 +1,11 @@
 """Methods for converting to/from HIF standard."""
 
+import math
 from collections import defaultdict
 
 from ..core import DiHypergraph, Hypergraph, SimplicialComplex
 from ..utils import IDDict
 from .bipartite_edges import to_bipartite_edgelist
-import math
 
 __all__ = ["to_hif_dict", "from_hif_dict"]
 

xgi/drawing/draw.py

@@ -1084,7 +1084,7 @@ def draw_node_labels(
 
     text_items = {}
     for idx, label in node_labels.items():
-        (x, y) = pos[idx]
+        x, y = pos[idx]
 
         if not isinstance(label, str):
             label = str(label)