risk-network 0.0.14b0__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.0"
+__version__ = "0.0.14-beta.2"

risk/_neighborhoods/_api.py

@@ -29,9 +29,6 @@ class NeighborhoodsAPI:
     The NeighborhoodsAPI class provides methods to load neighborhood results from statistical tests.
     """
 
-    def __init__(self) -> None:
-        pass
-
     def load_neighborhoods_binom(
         self,
         network: nx.Graph,

risk/_network/_graph/_api.py

@@ -27,9 +27,6 @@ class GraphAPI:
     The GraphAPI class provides methods to load and process network graphs, annotations, and neighborhoods.
     """
 
-    def __init__(self) -> None:
-        pass
-
     def load_graph(
         self,
         network: nx.Graph,

risk/_network/_io.py

@@ -24,24 +24,6 @@ class NetworkAPI:
     Delegates to the NetworkIO worker class for actual I/O and processing.
     """
 
-    def __init__(
-        self,
-        compute_sphere: bool = True,
-        surface_depth: float = 0.0,
-        min_edges_per_node: int = 0,
-    ):
-        """
-        Initialize the NetworkAPI.
-
-        Args:
-            compute_sphere (bool): Whether to map nodes to a sphere. Defaults to True.
-            surface_depth (float): Surface depth for the sphere. Defaults to 0.0.
-            min_edges_per_node (int): Minimum number of edges per node. Defaults to 0.
-        """
-        self.compute_sphere = compute_sphere
-        self.surface_depth = surface_depth
-        self.min_edges_per_node = min_edges_per_node
-
     def load_network_gpickle(
         self,
         filepath: str,
@@ -182,7 +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
@@ -458,20 +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/_plotter/_api.py

@@ -19,9 +19,6 @@ class PlotterAPI:
     The PlotterAPI class provides methods to load and configure Plotter objects for plotting network graphs.
     """
 
-    def __init__(self) -> None:
-        pass
-
     def load_plotter(
         self,
         graph: Graph,

{risk_network-0.0.14b0.dist-info → risk_network-0.0.14b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: risk-network
-Version: 0.0.14b0
+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-0.0.14b0.dist-info → risk_network-0.0.14b2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=4gUMRlMdNJ2feLptoxyeWymcTnqlyoExMrazTwzyfrs,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
@@ -8,7 +8,7 @@ risk/_log/__init__.py,sha256=LX6BsfcGOH0RbAdQaUmIU-LVMmArDdKwn0jFtj45FYo,205
 risk/_log/_console.py,sha256=1jSFzY3w0-vVqIBCgc-IhyJPNT6vRg8GSGxhyw_D9MI,4653
 risk/_log/_parameters.py,sha256=8FkeeBtULDFVw3UijLArK-G3OIjy6YXyRXmPPckK7fU,5893
 risk/_neighborhoods/__init__.py,sha256=eKwjpEUKSUmAirRZ_qPTVF7MLkvhCn_fulPVq158wM8,185
-risk/_neighborhoods/_api.py,sha256=6vt25y38wSvEhMvNxy9Rl-CrQc9ARSuvGwexWagg5z0,23344
+risk/_neighborhoods/_api.py,sha256=s1f4d_nEPWc66KDmOUUpRNXzp6dfoevw45ewOg9eMNo,23298
 risk/_neighborhoods/_community.py,sha256=Tr-EHO91EWbMmNr_z21UCngiqWOlWIqcjwBig_VXI8c,17850
 risk/_neighborhoods/_domains.py,sha256=He8G2-E9-yYQB8ChUtMFr51HVlfRj5EaxGu3sGVNUCo,14630
 risk/_neighborhoods/_neighborhoods.py,sha256=9H7BickJx9GdnOo5d5wpdtXkcWyvzq2w6FAy1rwLBtk,20614
@@ -18,14 +18,14 @@ 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=uiYmbKVsSRr4-TsY9KvRggDghtZv8qoxXac3QYs1lTI,28750
+risk/_network/_io.py,sha256=wmokwNViz24Gv6o3OFRTYHftYYz4sN64VigGrdEGzy8,28057
 risk/_network/_graph/__init__.py,sha256=SFgxgxUiZK4vvw6bdQ04DSMXEr8xjMaQV-Wne6wAIqM,104
-risk/_network/_graph/_api.py,sha256=zH7n-ulqLcbgHdAfLu1yWErdR5G4LgSqR7DcN2qApco,8520
+risk/_network/_graph/_api.py,sha256=sp3_mLJDP_xQexYBjyM17iyzLb2oGmiC050kcw-jVho,8474
 risk/_network/_graph/_graph.py,sha256=x2EWT_ZVwxh7m9a01yG4WMdmAxBxiaxX3CvkqP9QAXE,12486
 risk/_network/_graph/_stats.py,sha256=6mxZkuL6LJlwKDsBbP22DAVkNUEhq-JZwYMKhFKD08k,7359
 risk/_network/_graph/_summary.py,sha256=4eGhCArssePDg4LXr3sg5bUpNn7KFK9oPZcCz5lJKEQ,10334
 risk/_network/_plotter/__init__.py,sha256=qFRtQKSBGIqmUGwmA7VPL7hTHBb9yvRIt0nLISXnwkY,84
-risk/_network/_plotter/_api.py,sha256=MHZIMTlul2u-Ve5m9r-eUljI2oC3IRklNn7AVlfmzGs,1773
+risk/_network/_plotter/_api.py,sha256=OaV1CCRGsz98wEEzyEhaq2CqEuZh6t2qS7g_rY6HJJs,1727
 risk/_network/_plotter/_canvas.py,sha256=H7rPz4Gv7ED3bDHMif4cf2usdU4ifmxzXeug5A_no68,13599
 risk/_network/_plotter/_contour.py,sha256=E3ILjlv-VBSbK3ClwObB84TvP1D48_B47ODXwtApjIE,15557
 risk/_network/_plotter/_labels.py,sha256=8JXzEOIBQefwr1ngF-2ZYCnYLZXs2Erz-R1c28NnsL0,46915
@@ -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-0.0.14b0.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.14b0.dist-info/METADATA,sha256=rshHTAf4wXudUsCwUIQpK8VZzmb5-f_c9_fYfrYXdm0,6853
-risk_network-0.0.14b0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-risk_network-0.0.14b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.14b0.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,,