risk-network 0.0.9b16__py3-none-any.whl → 0.0.9b18__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.18"

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/plot/labels.py

@@ -564,39 +564,39 @@ class Labels:
 
         Returns:
             bool: True if the domain is valid and added to the filtered dictionaries, False otherwise.
-
-        Note:
-            The `filtered_domain_centroids`, `filtered_domain_terms`, and `valid_indices` are modified in-place.
         """
-        # Process the domain terms
-        domain_terms = self._process_terms(
-            domain=domain,
-            ids_to_labels=ids_to_labels,
-            words_to_omit=words_to_omit,
-            max_label_lines=max_label_lines,
-            min_chars_per_line=min_chars_per_line,
-            max_chars_per_line=max_chars_per_line,
-        )
-        # If domain_terms is empty, skip further processing
-        if not domain_terms:
-            return False
-
-        # Split the terms by TERM_DELIMITER and count the number of lines
-        num_domain_lines = len(domain_terms.split(TERM_DELIMITER))
-        # Check if the number of lines is greater than or equal to the minimum
-        if num_domain_lines >= min_label_lines:
-            filtered_domain_centroids[domain] = domain_centroid
-            filtered_domain_terms[domain] = domain_terms
-            # Add the index of the domain to the valid indices list
-            valid_indices.append(list(domain_id_to_centroid_map.keys()).index(domain))
-            return True
-
-        return False
+        if ids_to_labels and domain in ids_to_labels:
+            # Directly use custom labels without filtering
+            domain_terms = ids_to_labels[domain]
+        else:
+            # Process the domain terms automatically
+            domain_terms = self._process_terms(
+                domain=domain,
+                words_to_omit=words_to_omit,
+                max_label_lines=max_label_lines,
+                min_chars_per_line=min_chars_per_line,
+                max_chars_per_line=max_chars_per_line,
+            )
+            # If no valid terms are generated, skip further processing
+            if not domain_terms:
+                return False
+
+            # Split the terms by TERM_DELIMITER and count the number of lines
+            num_domain_lines = len(domain_terms.split(TERM_DELIMITER))
+            # Check if the number of lines meets the minimum requirement
+            if num_domain_lines < min_label_lines:
+                return False
+
+        # Store the valid terms and centroids
+        filtered_domain_centroids[domain] = domain_centroid
+        filtered_domain_terms[domain] = domain_terms
+        valid_indices.append(list(domain_id_to_centroid_map.keys()).index(domain))
+
+        return True
 
     def _process_terms(
         self,
         domain: str,
-        ids_to_labels: Union[Dict[int, str], None],
         words_to_omit: Union[List[str], None],
         max_label_lines: int,
         min_chars_per_line: int,
@@ -606,7 +606,6 @@ class Labels:
 
         Args:
             domain (str): The domain being processed.
-            ids_to_labels (Dict[int, str], None): Dictionary mapping domain IDs to custom labels.
             words_to_omit (List[str], None): List of words to omit from the labels.
             max_label_lines (int): Maximum number of lines in a label.
             min_chars_per_line (int): Minimum number of characters in a line to display.
@@ -615,13 +614,8 @@ class Labels:
         Returns:
             str: Processed terms separated by TERM_DELIMITER, with words combined if necessary to fit within constraints.
         """
-        # Return custom labels if domain is in ids_to_labels
-        if ids_to_labels and domain in ids_to_labels:
-            return ids_to_labels[domain]
-
-        else:
-            terms = self.graph.domain_id_to_domain_terms_map[domain].split(" ")
-
+        # Set custom labels from significant terms
+        terms = self.graph.domain_id_to_domain_terms_map[domain].split(" ")
         # Apply words_to_omit and word length constraints
         if words_to_omit:
             terms = [

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-0.0.9b18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b16
+Version: 0.0.9b18
 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-0.0.9b18.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=Y97538nwTi67cMHhP4b1tYJYhXdZHwHd4V63ET61HzA,127
+risk/__init__.py,sha256=9v2jfoqP2gtVfXHiTuxLNyDIkjAfdwBx1dv421Qem_w,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=nodTixy31O3VK7ld-g74Fb9YEiyvKs_Vbor2lE2ADJ8,23632
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
@@ -19,8 +19,8 @@ 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/labels.py,sha256=aU_ClDGVPHyQ3H5E_ygx8hsMhrpJB0i9Cn65PlLmw7s,45679
+risk/network/plot/contour.py,sha256=zM2oRbiGbKHi9fWL7QNcwnTRkxCuQYEwH2mm6TaN_hw,15499
+risk/network/plot/labels.py,sha256=fqBxQ1FoWI-la_7fEWAXWf0eaMWB01AeSasHYccf0gA,45452
 risk/network/plot/network.py,sha256=0j7pAZgt9PBfFCnOz4QwXnYWTlnLjTrtMm-50I_1G8o,14028
 risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
 risk/network/plot/utils/colors.py,sha256=9zuU2O-Nkpljb1yVGUR_IjqD1y-wH6Bf6Vm1MMVB0Lo,18718
@@ -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-0.0.9b18.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b18.dist-info/METADATA,sha256=p5vaR2ISJ8R2K6HG6IBH_MzKf2MVyFrnV3Q7o55TfnQ,47627
+risk_network-0.0.9b18.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b18.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b18.dist-info/RECORD,,