risk-network 0.0.9b16__tar.gz → 0.0.9b17__tar.gz

{risk_network-0.0.9b16 → risk_network-0.0.9b17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b16
+Version: 0.0.9b17
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b16 → risk_network-0.0.9b17}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.16"
+__version__ = "0.0.9-beta.17"

{risk_network-0.0.9b16 → risk_network-0.0.9b17}/risk/network/plot/contour.py

@@ -242,7 +242,7 @@ class Contour:
             logger.error("Contour levels must be strictly increasing. Skipping contour plot.")
             return None
 
-        # Set the contour color and linestyle
+        # Set the contour color, fill, and linestyle
         contour_colors = [color for _ in range(levels - 1)]
         # Plot the filled contours using fill_alpha for transparency
         if fill_alpha and fill_alpha > 0:
@@ -258,33 +258,19 @@ class Contour:
                 alpha=fill_alpha,
             )
 
-        # Plot the contour lines with the specified RGBA alpha for transparency
-        c = ax.contour(
+        # Plot the base contour line with the specified RGBA alpha for transparency
+        base_contour_color = [color]
+        base_contour_level = [contour_levels[0]]
+        ax.contour(
             x,
             y,
             z,
-            levels=contour_levels,
-            colors=contour_colors,
+            levels=base_contour_level,
+            colors=base_contour_color,
             linestyles=linestyle,
             linewidths=linewidth,
         )
 
-        # Set linewidth for the contour lines to 0 for levels other than the base level
-        c.set_linewidth(0)
-        try:
-            # Try setting linewidth directly on the QuadContourSet
-            c.set_linewidth(0)
-        except AttributeError:
-            # Fallback: Iterate over collections if the direct method fails
-            if hasattr(c, "collections"):
-                for i, collection in enumerate(c.collections):
-                    collection.set_linewidth(0)
-            else:
-                # Raise an error if 'collections' is also not available
-                raise AttributeError(
-                    "'QuadContourSet' object has neither 'set_linewidth' nor 'collections'"
-                )
-
     def get_annotated_contour_colors(
         self,
         cmap: str = "gist_rainbow",

{risk_network-0.0.9b16 → risk_network-0.0.9b17}/risk/stats/permutation/permutation.py

@@ -192,7 +192,9 @@ def _permutation_process_subset(
     local_counts_depletion = np.zeros(observed_neighborhood_scores.shape)
     local_counts_enrichment = np.zeros(observed_neighborhood_scores.shape)
 
-    # NOTE: Limit the number of threads used by NumPy's BLAS implementation to 1 when more than one worker is used.
+    # Limit the number of threads used by NumPy's BLAS implementation to 1 when more than one worker is used
+    # NOTE: This does not work for Mac M chips due to a bug in the threadpoolctl package
+    # This is currently a known issue and is being addressed by the maintainers [https://github.com/joblib/threadpoolctl/issues/135]
     limits = None if max_workers == 1 else 1
     with threadpool_limits(limits=limits, user_api="blas"):
         # Initialize a local counter for batched progress updates

{risk_network-0.0.9b16 → risk_network-0.0.9b17}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b16
+Version: 0.0.9b17
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>