Merge pull request #5 from dkaslovsky/eliminate_runtime_warning_for_l…

…og_calculation

Eliminate runtime warning for log calculation

.travis.yml

@@ -5,6 +5,7 @@ matrix:
     - python: 3.6
     - python: 3.7
     - python: 3.8
+    - python: 3.9
 
 install:
   - pip install -r requirements.txt

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 1.0.2 / 2021-06-26
+
+* [Fixed] eliminated runtime warning when computing log of array containing zeros
+* [Changed] added Python 3.9 support and updated necessary dependencies
+
 ## 1.0.1 / 2020-08-25
 
 * [Changed] updated dependencies to latest versions

graphrole/graph/interface/__init__.py

@@ -2,7 +2,6 @@
 
 from graphrole.graph.interface.base import BaseGraphInterface
 from graphrole.graph.interface.networkx import NetworkxInterface
-from graphrole.types import Edge, Node
 
 # IgraphInterface should not be imported if igraph is not installed
 try:
@@ -14,7 +13,7 @@
     'networkx': NetworkxInterface,
     # lazy eval in case IgraphInterface was not imported
     # pylint: disable=unnecessary-lambda
-    'igraph':   lambda x: IgraphInterface(x),
+    'igraph': lambda x: IgraphInterface(x),
 }
 
 

graphrole/graph/interface/base.py

@@ -55,4 +55,4 @@ def _get_egonet_features(self) -> pd.DataFrame:
         """
         Return egonet features for each node in the graph
         """
-        pass
+        pass

graphrole/graph/interface/igraph.py

@@ -155,7 +155,5 @@ def _is_boundary(self, edge: Edge, interior: Set[Node], exterior: Set[Node]) ->
             return v1 in interior and v2 in exterior
 
         return (
-            (v1 in interior and v2 in exterior)
-            or
-            (v1 in exterior and v2 in interior)
+            (v1 in interior and v2 in exterior) or (v1 in exterior and v2 in interior)
         )

graphrole/graph/interface/networkx.py

@@ -77,7 +77,6 @@ def _get_edge_sum(self, edges: Iterable[Edge]) -> float:
         :param edges: edges to sum
         """
         return sum(
-            self.G.get_edge_data(*edge, default={})\
-             .get('weight', 1)
+            self.G.get_edge_data(*edge, default={}).get('weight', 1)
             for edge in edges
         )

graphrole/roles/description_length.py

@@ -53,5 +53,9 @@ def get_error_cost(
     # KL divergence as given in section 2.3 of RolX paper
     vec1 = V.ravel()
     vec2 = V_approx.ravel()
-    kl_div = np.sum(np.where(vec1 != 0, vec1 * np.log(vec1 / vec2) - vec1 + vec2, 0))
+
+    # use mask in np.log to avoid runtime warning for zeros and in np.where to ensure correct value
+    mask = vec1 != 0
+    log_vals = np.log(vec1 / vec2, where=mask, out=np.zeros(vec1.shape))
+    kl_div = np.sum(np.where(mask, vec1 * log_vals - vec1 + vec2, 0))
     return kl_div

graphrole/roles/extract.py

@@ -91,7 +91,7 @@ def extract_role_factors(
             index=role_labels,
             columns=features.columns
         )
-    
+
     def explain(self):
         raise NotImplementedError('Role explanation (\"sense making\") is not yet implemented.')
 

requirements.txt

@@ -1,5 +1,6 @@
-networkx==2.5
-numpy==1.19.1
-pandas==1.1.1
-scikit-learn==0.23.2
-scipy==1.5.2
+networkx==2.5.1
+numpy==1.19.5
+pandas==1.1.5
+scikit-learn==0.24.2
+scipy==1.5.4
+

setup.py

@@ -10,7 +10,7 @@
 
 setup(
     name='graphrole',
-    version='1.0.1',
+    version='1.0.2',
     author='Daniel Kaslovsky',
     author_email='dkaslovsky@gmail.com',
     license='MIT',
@@ -32,5 +32,6 @@
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
     ]
 )