risk-network 0.0.9b31__py3-none-any.whl → 0.0.9b32__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.31"
+__version__ = "0.0.9-beta.32"

risk/stats/permutation/test_functions.py

@@ -46,19 +46,23 @@ def compute_neighborhood_score_by_stdev(
     neighborhood_score = neighborhoods_matrix @ annotation_matrix  # Sparse matrix multiplication
     # Calculate the number of elements in each neighborhood (sum of rows)
     N = neighborhoods_matrix.sum(axis=1).A.flatten()  # Convert to 1D array
-    # Avoid division by zero by replacing zeros in N with np.nan temporarily
-    N[N == 0] = np.nan
+    if np.any(N == 0):
+        # Replace zeros in N with small positive values to avoid division errors
+        N = np.where(N == 0, np.nan, N)
+
     # Compute the mean of the neighborhood scores
     M = neighborhood_score.multiply(1 / N[:, None]).toarray()  # Sparse element-wise division
     # Compute the mean of squares (EXX) directly using squared annotation matrix
     annotation_squared = annotation_matrix.multiply(annotation_matrix)  # Element-wise squaring
     EXX = (neighborhoods_matrix @ annotation_squared).multiply(1 / N[:, None]).toarray()
-    # Calculate variance as EXX - M^2
-    variance = EXX - np.power(M, 2)
+
+    # Calculate variance as EXX - M^2, ensuring no negative variances
+    variance = np.maximum(EXX - np.power(M, 2), 0)
     # Compute the standard deviation as the square root of the variance
     neighborhood_stdev = np.sqrt(variance)
-    # Replace np.nan back with zeros in case N was 0 (no elements in the neighborhood)
+    # Replace np.nan back with zeros for rows where N was 0
     neighborhood_stdev[np.isnan(neighborhood_stdev)] = 0
+
     return neighborhood_stdev
 
 

{risk_network-0.0.9b31.dist-info → risk_network-0.0.9b32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b31
+Version: 0.0.9b32
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b31.dist-info → risk_network-0.0.9b32.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=u9we76elYKA9qWrJZg4C-XZbyChmetziqTr0kOIDH18,127
+risk/__init__.py,sha256=qajW0v2X0MIHZ7-xLzacsw7D5QIhAUNYIMV5sbIS7o4,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=s827_lRknFseOP9O4zW8sP-IcCd2EzrpV_tnVY_tz5s,1104
 risk/annotations/__init__.py,sha256=parsbcux1U4urpUqh9AdzbDWuLj9HlMidycMPkpSQFo,179
@@ -33,9 +33,9 @@ risk/stats/significance.py,sha256=6cKv2xBQXWTHZ6HpNWIqlNfKKS5pG_BcCUdMM3r_zw4,73
 risk/stats/stat_tests.py,sha256=MR59l5k0i5AiEIjPFPKIKHcj_nQ2wxvwW4eqYV7jOa0,11776
 risk/stats/permutation/__init__.py,sha256=OLmYLm2uj96hPsSaUs0vUqFYw6Thwch_aHtpL7L0ZFw,127
 risk/stats/permutation/permutation.py,sha256=BWjgdBpLVcHvmwHy0bmD4aJFccxifNBSrrCBPppyKf4,10569
-risk/stats/permutation/test_functions.py,sha256=D3XMPM8CasUNytWSRce22TI6KK6XulYn5uGG4lWxaHs,3120
-risk_network-0.0.9b31.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b31.dist-info/METADATA,sha256=cX2PA1RUzQx0gTvycUyJBiolwlIxQKtzuCQQmHnGYn0,47627
-risk_network-0.0.9b31.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-risk_network-0.0.9b31.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b31.dist-info/RECORD,,
+risk/stats/permutation/test_functions.py,sha256=WQpSIkCsaAMolkFUWbL58l_a4V9wUT7eyHbKKEXNGsU,3187
+risk_network-0.0.9b32.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b32.dist-info/METADATA,sha256=0x1A_lAgtqv9qxhRkQ_aH0jTxyIBdNPYoCwX6dsjjaQ,47627
+risk_network-0.0.9b32.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b32.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b32.dist-info/RECORD,,