risk-network 0.0.14b1__py3-none-any.whl → 0.0.14b2__py3-none-any.whl

risk/__init__.py

@@ -8,4 +8,4 @@ RISK: Regional Inference of Significant Kinships
 from ._risk import RISK
 
 __all__ = ["RISK"]
-__version__ = "0.0.14-beta.1"
+__version__ = "0.0.14-beta.2"

risk/_network/_io.py

@@ -164,7 +164,7 @@ class NetworkIO:
         Args:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
-            min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
+            min_edges_per_node (int, optional): Minimum number of edges per node (k-core threshold). Defaults to 0.
         """
         self.compute_sphere = compute_sphere
         self.surface_depth = surface_depth
@@ -440,20 +440,14 @@ class NetworkIO:
         num_initial_edges = G.number_of_edges()
         # Remove self-loops to ensure correct edge count
         G.remove_edges_from(nx.selfloop_edges(G))
-        # Iteratively remove nodes with fewer edges than the threshold
-        while True:
-            nodes_to_remove = [
-                node
-                for node, degree in dict(G.degree()).items()
-                if degree < self.min_edges_per_node
-            ]
-            if not nodes_to_remove:
-                break  # Exit loop if no nodes meet the condition
-            G.remove_nodes_from(nodes_to_remove)
-
-        # Remove isolated nodes
-        isolates = list(nx.isolates(G))
-        G.remove_nodes_from(isolates)
+        # Apply canonical node k-core pruning if requested
+        if self.min_edges_per_node > 0:
+            # networkx.k_core returns a subgraph; to preserve in-place behavior, copy back
+            core = nx.k_core(G, k=self.min_edges_per_node)
+            # Rebuild G in-place to keep external references valid
+            G.clear()
+            G.add_nodes_from(core.nodes(data=True))
+            G.add_edges_from(core.edges(data=True))
 
         # Log the number of nodes and edges before and after cleaning
         num_final_nodes = G.number_of_nodes()

{risk_network-0.0.14b1.dist-info → risk_network-0.0.14b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.14b1
+Version: 0.0.14b2
 Summary: A Python package for scalable network analysis and high-quality visualization.
 Author-email: Ira Horecka <ira89@icloud.com>
 License: GPL-3.0-or-later

{risk_network-0.0.14b1.dist-info → risk_network-0.0.14b2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=EhZWpNfkex4HOMUEdfleuQ78CzIktejWJnpn8TdWr6Q,143
+risk/__init__.py,sha256=Kit6ilMaj_3F16dnLJ_Dd7fE5jeZGmNqur97zzK7CRI,143
 risk/_risk.py,sha256=VULCdM41BlWKM1ou4Qc579ffZ9dMZkfhAwKYgbaEeKM,1054
 risk/_annotation/__init__.py,sha256=zr7w1DHkmvrkKFGKdPhrcvZHV-xsfd5TZOaWtFiP4Dc,164
 risk/_annotation/_annotation.py,sha256=03vcnkdi4HGH5UUyokUyOdyyjXOLoKSmLFuK7VAl41c,15174
@@ -18,7 +18,7 @@ risk/_neighborhoods/_stats/_permutation/__init__.py,sha256=nfTaW29CK8OZCdFnpMVlH
 risk/_neighborhoods/_stats/_permutation/_permutation.py,sha256=e5qVuYWGhiAn5Jv8VILk-WYMOO4km48cGdRYTOl355M,10661
 risk/_neighborhoods/_stats/_permutation/_test_functions.py,sha256=lGI_MkdbW4UHI0jWN_T1OattRjXrq_qmzAmOfels670,3165
 risk/_network/__init__.py,sha256=YrAMfhL0CMWQb3sY-mn1VxK44zZAWeFAvHrBONH9I-A,127
-risk/_network/_io.py,sha256=wjy_wkQkRO4sI_U6Xvheu7x_Jd8mXyBnXAhtZSjqJHY,28129
+risk/_network/_io.py,sha256=wmokwNViz24Gv6o3OFRTYHftYYz4sN64VigGrdEGzy8,28057
 risk/_network/_graph/__init__.py,sha256=SFgxgxUiZK4vvw6bdQ04DSMXEr8xjMaQV-Wne6wAIqM,104
 risk/_network/_graph/_api.py,sha256=sp3_mLJDP_xQexYBjyM17iyzLb2oGmiC050kcw-jVho,8474
 risk/_network/_graph/_graph.py,sha256=x2EWT_ZVwxh7m9a01yG4WMdmAxBxiaxX3CvkqP9QAXE,12486
@@ -34,8 +34,8 @@ risk/_network/_plotter/_plotter.py,sha256=F2hw-spUdsXjvuG36o0YFR3Pnd-CZOHYUq4vW0
 risk/_network/_plotter/_utils/__init__.py,sha256=JXgjKiBWvXx0X2IeFnrOh5YZQGQoELbhJZ0Zh2mFEOo,211
 risk/_network/_plotter/_utils/_colors.py,sha256=JCliSvz8_-TsjilaRHSEsqdXFBUYlzhXKOSRGdCm9Kw,19177
 risk/_network/_plotter/_utils/_layout.py,sha256=GyGLc2U1WWUVL1Te9uPi_CLqlW_E4TImXRAL5TeA5D8,3633
-risk_network-0.0.14b1.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.14b1.dist-info/METADATA,sha256=82-RZi0eyLscZ5PG64zxheyTSVCb36LkV2GXE7Kmf44,6853
-risk_network-0.0.14b1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-risk_network-0.0.14b1.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.14b1.dist-info/RECORD,,
+risk_network-0.0.14b2.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.14b2.dist-info/METADATA,sha256=8Ymwky3eLiYB9OMO0kVzfF40uvnD3uFCBmY7q6pfitI,6853
+risk_network-0.0.14b2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+risk_network-0.0.14b2.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.14b2.dist-info/RECORD,,