Merge pull request #35 from saibalmars/fix_karate_weight

Update POT api

Author: saibalmars

.github/workflows/build.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
         os: [ubuntu-latest, macOS-latest]
         include:
           - os: ubuntu-latest

GraphRicciCurvature/OllivierRicci.py

@@ -247,7 +247,7 @@ def _sinkhorn_distance(x, y, d):
 
     """
     t0 = time.time()
-    m = ot.sinkhorn2(x, y, d, 1e-1, method='sinkhorn')[0]
+    m = ot.sinkhorn2(x, y, d, 1e-1, method='sinkhorn')
     logger.debug(
         "%8f secs for Sinkhorn dist. \t#source_nbr: %d, #target_nbr: %d" % (time.time() - t0, len(x), len(y)))
 

GraphRicciCurvature/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "0.5.3"
+__version__ = "0.5.3.1"
 __author__ = "Chien-Chun Ni"
 __email__ = "saibalmars@gmail.com"

notebooks/tutorial.ipynb

@@ -102,7 +102,8 @@
    "source": [
     "### Load sample graph\n",
     "\n",
-    "- First, let's load karate club graph from networkx as an example."
+    "- First, let's load karate club graph from networkx as an example.\n",
+    "- Ricci curavture and Ricci flow supported weighted graph, but for simplification, let's start from the unweighted graph first."
    ]
   },
   {
@@ -119,7 +120,9 @@
    },
    "outputs": [],
    "source": [
-    "G = nx.karate_club_graph()"
+    "G = nx.karate_club_graph()\n",
+    "for (n1, n2, d) in G.edges(data=True):\n",
+    "    d.clear()   # remove edge weight "
    ]
   },
   {
@@ -1748,7 +1751,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1762,7 +1765,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

requirements.txt

@@ -2,7 +2,7 @@ cython
 numpy
 scipy>=1.0
 networkx>=2.0
-pot
+pot>=0.8.0
 packaging
 networkit>=6.1
 python-louvain

setup.py

@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="GraphRicciCurvature",
-    version="0.5.3",
+    version="0.5.3.1",
     author="Chien-Chun Ni",
     author_email="saibalmars@gmail.com",
     description="Compute discrete Ricci curvatures and Ricci flow on NetworkX graphs.",

test/test_OllivierRicci.py

@@ -6,6 +6,8 @@
 
 def test_compute_ricci_curvature_edges():
     G = nx.karate_club_graph()
+    for (n1, n2, d) in G.edges(data=True):
+        d.clear()   # remove edge weight
     orc = OllivierRicci(G, method="OTD", alpha=0.5)
     output = orc.compute_ricci_curvature_edges([(0, 1)])
 
@@ -14,6 +16,8 @@ def test_compute_ricci_curvature_edges():
 
 def test_compute_ricci_curvature():
     G = nx.karate_club_graph()
+    for (n1, n2, d) in G.edges(data=True):
+        d.clear()   # remove edge weight
     orc = OllivierRicci(G, method="OTD", alpha=0.5)
     Gout = orc.compute_ricci_curvature()
     rc = list(nx.get_edge_attributes(Gout, "ricciCurvature").values())
@@ -46,6 +50,8 @@ def test_compute_ricci_curvature_directed():
 
 def test_compute_ricci_curvature_ATD():
     G = nx.karate_club_graph()
+    for (n1, n2, d) in G.edges(data=True):
+        d.clear()   # remove edge weight
     orc = OllivierRicci(G, alpha=0.5, method="ATD", verbose="INFO")
     orc.compute_ricci_curvature()
     Gout = orc.compute_ricci_curvature()
@@ -65,6 +71,8 @@ def test_compute_ricci_curvature_ATD():
 
 def test_compute_ricci_flow():
     G = nx.karate_club_graph()
+    for (n1, n2, d) in G.edges(data=True):
+        d.clear()   # remove edge weight
     orc = OllivierRicci(G, method="OTD", alpha=0.5)
     Gout = orc.compute_ricci_flow(iterations=3)
     rf = list(nx.get_edge_attributes(Gout, "weight").values())
@@ -82,6 +90,8 @@ def test_compute_ricci_flow():
 
 def test_ricci_community_all_possible_clusterings():
     G = nx.karate_club_graph()
+    for (n1, n2, d) in G.edges(data=True):
+        d.clear()   # remove edge weight
     orc = OllivierRicci(G, exp_power=1, alpha=0.5)
     orc.compute_ricci_flow(iterations=40)
     cc = orc.ricci_community_all_possible_clusterings()
@@ -117,6 +127,8 @@ def test_ricci_community_all_possible_clusterings():
 
 def test_ricci_community():
     G = nx.karate_club_graph()
+    for (n1, n2, d) in G.edges(data=True):
+        d.clear()   # remove edge weight
     orc = OllivierRicci(G, exp_power=1, alpha=0.5)
     cut, clustering = orc.ricci_community()
     cut_ans = 1.2613588421005884