risk-network 0.0.14b0__tar.gz → 0.0.14b2__tar.gz

{risk_network-0.0.14b0/src/risk_network.egg-info → risk_network-0.0.14b2}/PKG-INFO

@@ -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 → risk_network-0.0.14b2}/src/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_network-0.0.14b0 → risk_network-0.0.14b2}/src/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-0.0.14b0 → risk_network-0.0.14b2}/src/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-0.0.14b0 → risk_network-0.0.14b2}/src/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-0.0.14b0 → risk_network-0.0.14b2}/src/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 → risk_network-0.0.14b2/src/risk_network.egg-info}/PKG-INFO

@@ -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 → risk_network-0.0.14b2}/tests/test_load_network.py

@@ -251,7 +251,7 @@ def test_attribute_fallback_mechanism(risk_obj, data_path):
 @pytest.mark.parametrize("min_edges", [1, 5, 10])
 def test_load_network_min_edges(risk_obj, data_path, min_edges):
     """
-    Test loading a Cytoscape network with varying min_edges_per_node.
+    Test loading a Cytoscape network with varying min_edges_per_node using canonical k-core pruning.
 
     Args:
         risk_obj: The RISK object instance used for loading the network.
@@ -399,7 +399,7 @@ def test_missing_node_attributes(risk_obj, cytoscape_network):
 
 def test_remove_isolates_does_not_raise(risk_obj, dummy_network):
     """
-    Test that loading a network with isolated nodes does not raise an error.
+    Test that canonical k-core removal (via min_edges_per_node) handles isolated nodes without error.
 
     Args:
         risk_obj: The RISK object instance used for loading the network.