risk-network 0.0.9b2__py3-none-any.whl → 0.0.9b3__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.2"
+__version__ = "0.0.9-beta.3"

risk/network/graph/network.py

@@ -10,7 +10,7 @@ import networkx as nx
 import numpy as np
 import pandas as pd
 
-from risk.network.graph.summary import Summary
+from risk.network.graph.summary import AnalysisSummary
 
 
 class NetworkGraph:
@@ -73,7 +73,7 @@ class NetworkGraph:
         self.node_coordinates = _extract_node_coordinates(self.network)
 
         # NOTE: Only after the above attributes are initialized, we can create the summary
-        self.summary = Summary(annotations, neighborhoods, self)
+        self.summary = AnalysisSummary(annotations, neighborhoods, self)
 
     @staticmethod
     def _create_domain_id_to_node_ids_map(domains: pd.DataFrame) -> Dict[int, Any]:

risk/network/graph/summary.py

@@ -3,8 +3,6 @@ risk/network/graph/summary
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
-import warnings
-from functools import lru_cache
 from typing import Any, Dict, Tuple, Union
 
 import numpy as np
@@ -14,11 +12,7 @@ from statsmodels.stats.multitest import fdrcorrection
 from risk.log.console import logger, log_header
 
 
-# Suppress all warnings - this is to resolve warnings from multiprocessing
-warnings.filterwarnings("ignore")
-
-
-class Summary:
+class AnalysisSummary:
     """Handles the processing, storage, and export of network analysis results.
 
     The Results class provides methods to process significance and depletion data, compute
@@ -79,7 +73,6 @@ class Summary:
 
         logger.info(f"Results summary exported to text file: {filepath}")
 
-    @lru_cache(maxsize=None)
     def load(self) -> pd.DataFrame:
         """Load and process domain and annotation data into a DataFrame with significance metrics.
 
@@ -91,7 +84,7 @@ class Summary:
             pd.DataFrame: Processed DataFrame containing significance scores, p-values, q-values,
                 and annotation member information.
         """
-        log_header("Loading parameters")
+        log_header("Loading analysis summary")
         # Calculate significance and depletion q-values from p-value matrices in `annotations`
         enrichment_pvals = self.neighborhoods["enrichment_pvals"]
         depletion_pvals = self.neighborhoods["depletion_pvals"]
@@ -132,12 +125,12 @@ class Summary:
             result_type="expand",
         )
         # Add annotation members and their counts
-        results["Annotation Members"] = results["Annotation"].apply(
+        results["Annotation Members in Network"] = results["Annotation"].apply(
             lambda desc: self._get_annotation_members(desc)
         )
-        results["Annotation Member Count"] = results["Annotation Members"].apply(
-            lambda x: len(x.split(";")) if x else 0
-        )
+        results["Annotation Member in Network Count"] = results[
+            "Annotation Members in Network"
+        ].apply(lambda x: len(x.split(";")) if x else 0)
 
         # Reorder columns and drop rows with NaN values
         results = (
@@ -145,8 +138,8 @@ class Summary:
                 [
                     "Domain ID",
                     "Annotation",
-                    "Annotation Members",
-                    "Annotation Member Count",
+                    "Annotation Members in Network",
+                    "Annotation Member in Network Count",
                     "Summed Significance Score",
                     "Enrichment P-value",
                     "Enrichment Q-value",
@@ -230,6 +223,7 @@ class Summary:
         except ValueError:
             return ""  # Description not found
 
+        # Get nodes present for the annotation and sort by node label
         nodes_present = np.where(self.annotations["matrix"][:, annotation_idx] == 1)[0]
         node_labels = sorted(
             self.graph.node_id_to_node_label_map[node_id]

{risk_network-0.0.9b2.dist-info → risk_network-0.0.9b3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b2
+Version: 0.0.9b3
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b2.dist-info → risk_network-0.0.9b3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=ICwmPcHgPSGMULpN30hPbaL4pu5GlN6TVBB5aduUyVM,112
+risk/__init__.py,sha256=japxenqMvqgfrLH-PHOulkDBiW_CZRMVUaDbR92setc,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=De1vn8Xc-TKz6aTL0bvJI-SVrIqU3k0IWAbKc7dde1c,23618
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
@@ -15,8 +15,8 @@ risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=gFtYUj9j9aul4paKq_qSGJn39Nazxu_MXv8m-tYYtrk,6840
 risk/network/io.py,sha256=AWSbZGLZHtl72KSlafQlcYoG00YLSznG7UYDi_wDT7M,22958
 risk/network/graph/__init__.py,sha256=H0YEiwqZ02LBTkH4blPwUjQ-DOUnhaTTNHM0BcXii6U,81
-risk/network/graph/network.py,sha256=4tDtQExFo9U1smaaxf-CaoxHOY99aagM2G11ap_DKbY,10192
-risk/network/graph/summary.py,sha256=zxkI9VyrYN5y41jlqLOIcDX0fF4wt24khtr6to36_uc,9239
+risk/network/graph/network.py,sha256=o7Rdp2S8cxYiT90IvGLqsn93wq9YA1vKRZ7fedLUir0,10208
+risk/network/graph/summary.py,sha256=f4j-ERlddzAhd9qEELiGdzmPqpzgoRODyHNe9QuRT7k,9190
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
 risk/network/plot/canvas.py,sha256=TlCpNtvoceizAumNr9I02JcBrBO6FiAFAa2ZC0bx3SU,13356
 risk/network/plot/contour.py,sha256=2ZVOlduo4Y4yIpXDJMIKO-v7eULcJ2QacQyOc7pUAxE,15267
@@ -32,8 +32,8 @@ risk/stats/stats.py,sha256=z8NrhiVj4BzJ250bVLfytpmfC7RzYu7mBuIZD_l0aCA,7222
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=meBNSrbRa9P8WJ54n485l0H7VQJlMSfHqdN4aCKYCtQ,10105
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b2.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b2.dist-info/METADATA,sha256=ccV7eOOwXIFCkiyfNIvCwLkTNQed1DuOmwXL84Nx2dY,47497
-risk_network-0.0.9b2.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b2.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b2.dist-info/RECORD,,
+risk_network-0.0.9b3.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b3.dist-info/METADATA,sha256=nUhDrkDb3ZbsCcKRxKOgx6yL6t1FHK4SRbrQNjdktII,47497
+risk_network-0.0.9b3.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.9b3.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b3.dist-info/RECORD,,