napistu 0.3.4__tar.gz → 0.3.5__tar.gz

{napistu-0.3.4 → napistu-0.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.4
+Version: 0.3.5
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett

{napistu-0.3.4 → napistu-0.3.5}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napistu
-version = 0.3.4
+version = 0.3.5
 description = Connecting high-dimensional data to curated pathways
 long_description = file: README.md
 long_description_content_type = text/markdown

{napistu-0.3.4 → napistu-0.3.5}/src/napistu/constants.py

@@ -149,10 +149,10 @@ INTERACTION_EDGELIST_EXPECTED_VARS = {
     "downstream_name",
     "upstream_compartment",
     "downstream_compartment",
-    "r_name",
-    "sbo_term",
-    "r_Identifiers",
-    "r_isreversible",
+    SBML_DFS.R_NAME,
+    SBML_DFS.SBO_TERM,
+    SBML_DFS.R_IDENTIFIERS,
+    SBML_DFS.R_ISREVERSIBLE,
 }
 
 BQB_PRIORITIES = pd.DataFrame(

{napistu-0.3.4 → napistu-0.3.5}/src/napistu/network/ig_utils.py

@@ -99,6 +99,41 @@ def filter_to_largest_subgraph(graph: ig.Graph) -> ig.Graph:
     return largest_subgraph
 
 
+def filter_to_largest_subgraphs(graph: ig.Graph, top_k: int) -> list[ig.Graph]:
+    """
+    Filter an igraph to its largest weakly connected components.
+
+    Parameters
+    ----------
+    graph : ig.Graph
+        The input network.
+    top_k : int
+        The number of largest components to return.
+
+    Returns
+    -------
+    list[ig.Graph]
+        A list of the top K largest components as graphs.
+    """
+    if top_k < 1:
+        raise ValueError("top_k must be 1 or greater.")
+
+    component_members = graph.components(mode="weak")
+    if not component_members:
+        return []
+
+    component_sizes = [len(x) for x in component_members]
+
+    # Sort components by size in descending order
+    sorted_components = sorted(
+        zip(component_sizes, component_members), key=lambda x: x[0], reverse=True
+    )
+
+    # Return a list of the top K subgraphs
+    top_k_components = sorted_components[:top_k]
+    return [graph.induced_subgraph(members) for _, members in top_k_components]
+
+
 def graph_to_pandas_dfs(graph: ig.Graph) -> tuple[pd.DataFrame, pd.DataFrame]:
     """
     Convert an igraph to Pandas DataFrames for vertices and edges.

{napistu-0.3.4 → napistu-0.3.5}/src/napistu/network/precompute.py

@@ -4,6 +4,7 @@ import logging
 import math
 from pathlib import Path
 from typing import Union
+import io
 
 import numpy as np
 import pandas as pd
@@ -144,7 +145,7 @@ def load_precomputed_distances(uri: Union[str, Path]) -> pd.DataFrame:
     """
     try:
         json_string = load_json(str(uri))
-        df = pd.read_json(json_string)
+        df = pd.read_json(io.StringIO(json_string))
 
         # Convert integer columns to float
         for col in df.columns: