risk-network 0.0.9b16__py3-none-any.whl → 0.0.9b17__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.16"
+__version__ = "0.0.9-beta.17"

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/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.dist-info → risk_network-0.0.9b17.dist-info}/METADATA

@@ -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.dist-info → risk_network-0.0.9b17.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=Y97538nwTi67cMHhP4b1tYJYhXdZHwHd4V63ET61HzA,127
+risk/__init__.py,sha256=95ug0762a0OMBkPuFt_fuQuF8BgPXRfF_Dl3UCP6jMw,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=nodTixy31O3VK7ld-g74Fb9YEiyvKs_Vbor2lE2ADJ8,23632
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
@@ -19,7 +19,7 @@ risk/network/graph/network.py,sha256=JzYbrgJLiNWFyPIR6_qNSjMtmXmfzRv2FwWSdyg8HjY
 risk/network/graph/summary.py,sha256=7w5gNYNspv02SscDAfHxdx-D1CWKmelSonyBnB9hbrE,9737
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
 risk/network/plot/canvas.py,sha256=W8dFv4XYTzCWXBchgsc0esOQRn4usM4LkwNGPSDMobE,13357
-risk/network/plot/contour.py,sha256=1Didhg9Z5seqdEITxWo7Av-Jg_TAuIHv_rPTMQZpkqo,16123
+risk/network/plot/contour.py,sha256=zM2oRbiGbKHi9fWL7QNcwnTRkxCuQYEwH2mm6TaN_hw,15499
 risk/network/plot/labels.py,sha256=aU_ClDGVPHyQ3H5E_ygx8hsMhrpJB0i9Cn65PlLmw7s,45679
 risk/network/plot/network.py,sha256=0j7pAZgt9PBfFCnOz4QwXnYWTlnLjTrtMm-50I_1G8o,14028
 risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
@@ -30,10 +30,10 @@ risk/stats/hypergeom.py,sha256=oc39f02ViB1vQ-uaDrxG_tzAT6dxQBRjc88EK2EGn78,2282
 risk/stats/poisson.py,sha256=polLgwS08MTCNzupYdmMUoEUYrJOjAbcYtYwjlfeE5Y,1803
 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/permutation.py,sha256=jfo7J7bjXTHH-k6_WuZ_5eB31JVynlI6SYMC_7icYyM,10320
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b16.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b16.dist-info/METADATA,sha256=pGpChS9mrqjv7i21ReWmVdOK0VyuLoB9HmhDrRupWSY,47627
-risk_network-0.0.9b16.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-risk_network-0.0.9b16.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b16.dist-info/RECORD,,
+risk_network-0.0.9b17.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b17.dist-info/METADATA,sha256=7Jh5RwTtOR7nnQIoLnT6wCamrgaAJxAZs6Zzncs0H9g,47627
+risk_network-0.0.9b17.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b17.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b17.dist-info/RECORD,,