risk-network 0.0.9b25__tar.gz → 0.0.9b26__tar.gz

{risk_network-0.0.9b25 → risk_network-0.0.9b26}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b25
+Version: 0.0.9b26
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b25 → risk_network-0.0.9b26}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.25"
+__version__ = "0.0.9-beta.26"

{risk_network-0.0.9b25 → risk_network-0.0.9b26}/risk/neighborhoods/domains.py

@@ -39,6 +39,9 @@ def define_domains(
         pd.DataFrame: DataFrame with the primary domain for each node.
     """
     try:
+        if linkage_criterion == "off":
+            raise ValueError("Clustering is turned off.")
+
         # Transpose the matrix to cluster annotations
         m = significant_neighborhoods_significance[:, top_annotations["significant_annotations"]].T
         # Safeguard the matrix by replacing NaN, Inf, and -Inf values
@@ -62,9 +65,14 @@ def define_domains(
     except ValueError:
         # If a ValueError is encountered, handle it by assigning unique domains
         n_rows = len(top_annotations)
-        logger.error(
-            f"Error encountered. Skipping clustering and assigning {n_rows} unique domains."
-        )
+        if linkage_criterion == "off":
+            logger.warning(
+                f"Clustering is turned off. Skipping clustering and assigning {n_rows} unique domains."
+            )
+        else:
+            logger.error(
+                f"Error encountered. Skipping clustering and assigning {n_rows} unique domains."
+            )
         top_annotations["domain"] = range(1, n_rows + 1)  # Assign unique domains
 
     # Create DataFrames to store domain information

{risk_network-0.0.9b25 → risk_network-0.0.9b26}/risk/stats/permutation/permutation.py

@@ -95,7 +95,7 @@ def _run_permutation_test(
     if null_distribution == "network":
         idxs = range(annotations.shape[0])
     elif null_distribution == "annotations":
-        idxs = np.nonzero(np.sum(~np.isnan(annotations), axis=1))[0]
+        idxs = np.nonzero(annotations.getnnz(axis=1) > 0)[0]
     else:
         raise ValueError(
             "Invalid null_distribution value. Choose either 'network' or 'annotations'."

{risk_network-0.0.9b25 → risk_network-0.0.9b26}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b25
+Version: 0.0.9b26
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>