Pull request #209: Hotfix/test lint

Merge in HYP/hypernetx from hotfix/test-lint to develop

* commit '10bd14e70d99f96dd3c841289f909769c25d6c62':
  bump: version 2.3.5 → 2.3.6
  pre-commit edits
  remove numpy required version
  fixed some typos and updated the version of scipy
  updated test suite to use .toarray instead of .A to transform csr_matrix to numpy array
  pre-commit and version tag
  pre-commit and version tag

.cz.toml

@@ -1,6 +1,6 @@
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "2.3.5"
+version = "2.3.6"
 version_provider = "poetry"
 version_files = [
     "pyproject.toml",

docs/source/conf.py

@@ -19,7 +19,7 @@
 import os
 
 
-__version__ = "2.3.5"
+__version__ = "2.3.6"
 
 
 # If extensions (or modules to document with autodoc) are in another directory,

hypernetx/__init__.py

@@ -11,4 +11,4 @@
 from hypernetx.utils import *
 from hypernetx.utils.toys import *
 
-__version__ = "2.3.5"
+__version__ = "2.3.6"

hypernetx/algorithms/hypergraph_modularity.py

@@ -183,7 +183,11 @@ def modularity(HG, A, wdc=linear):
         _df = pd.DataFrame(zip(_keys, _vals), columns=["key", "val"])
         _df = _df.groupby(by="key").sum()
         EC = sum(
-            [wdc(k[1], k[0]) * v.iloc[0] for (k, v) in _df.iterrows() if k[0] > k[1] / 2]
+            [
+                wdc(k[1], k[0]) * v.iloc[0]
+                for (k, v) in _df.iterrows()
+                if k[0] > k[1] / 2
+            ]
         )
 
     ## Degree Tax
@@ -294,8 +298,8 @@ def two_section(HG):
     G = ig.Graph.TupleList(s, weights=True).simplify(combine_edges="sum")
 
     ## add isolates if any
-    isolates = list(set([v for v in HG.nodes]) - set(G.vs['name']))
-    if len(isolates)>0:
+    isolates = list(set([v for v in HG.nodes]) - set(G.vs["name"]))
+    if len(isolates) > 0:
         G.add_vertices(isolates)
 
     return G

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hypernetx"
-version = "2.3.5"
+version = "2.3.6"
 description = "HyperNetX is a Python library for the creation and study of hypergraphs."
 authors = ["Brenda Praggastis <[email protected]>", "Dustin Arendt <[email protected]>",
     "Sinan Aksoy <[email protected]>", "Emilie Purvine <[email protected]>",
@@ -29,6 +29,7 @@ scikit-learn = ">=1.4.2"
 celluloid = ">=0.2.0"
 igraph = ">=0.11.4"
 decorator = ">=5.1.1"
+scipy = ">=1.13"
 
 [tool.poetry.group.widget]
 optional = true

tests/classes/conftest.py

@@ -86,7 +86,7 @@ def __init__(self):
                 [0, 0, 0, 0, 0, 1],
             ]
         )
-        self.s1_adjacency_matrx = scipy.sparse.csr_matrix(
+        self.s1_adjacency_matrix = scipy.sparse.csr_matrix(
             [
                 [0, 1, 1, 1, 0, 1, 1],
                 [1, 0, 1, 1, 0, 0, 0],
@@ -97,7 +97,7 @@ def __init__(self):
                 [1, 0, 0, 1, 0, 1, 0],
             ]
         )
-        self.s1_edge_adjacency_matrx = scipy.sparse.csr_matrix(
+        self.s1_edge_adjacency_matrix = scipy.sparse.csr_matrix(
             [
                 [0, 0, 1, 1, 0, 1],
                 [0, 0, 0, 1, 1, 0],

tests/classes/test_hypergraph.py

@@ -1093,7 +1093,9 @@ def test_incidence_matrix(sevenbysix):
         len(sevenbysix.nodes),
         len(sevenbysix.edges),
     )
-    assert np.allclose(incidence_matrix.A, sevenbysix.incidence_matrix.A)
+    assert np.allclose(
+        incidence_matrix.toarray(), sevenbysix.incidence_matrix.toarray()
+    )
 
     # check the edge and node indexes
     assert nodes_idx.tolist() == list(sevenbysix.nodes)
@@ -1109,7 +1111,9 @@ def test_adjacency_matrix(sevenbysix):
         len(sevenbysix.nodes),
         len(sevenbysix.nodes),
     )
-    assert np.allclose(adjacency_matrix.A, sevenbysix.s1_adjacency_matrx.A)
+    assert np.allclose(
+        adjacency_matrix.toarray(), sevenbysix.s1_adjacency_matrix.toarray()
+    )
     assert node_idx.tolist() == list(sevenbysix.nodes)
 
 
@@ -1122,7 +1126,9 @@ def test_edge_adjacency_matrix(sevenbysix):
         len(sevenbysix.edges),
         len(sevenbysix.edges),
     )
-    assert np.allclose(adjacency_matrix.A, sevenbysix.s1_edge_adjacency_matrx.A)
+    assert np.allclose(
+        adjacency_matrix.toarray(), sevenbysix.s1_edge_adjacency_matrix.toarray()
+    )
     assert node_idx.tolist() == list(sevenbysix.edges)
 
 
@@ -1132,7 +1138,7 @@ def test_auxiliary_matrix_on_nodes(sevenbysix):
     aux_matrix, indexes = hg.auxiliary_matrix(index=True)
 
     assert aux_matrix.todense().shape == (len(sevenbysix.nodes), len(sevenbysix.nodes))
-    assert np.allclose(aux_matrix.A, sevenbysix.s1_adjacency_matrx.A)
+    assert np.allclose(aux_matrix.toarray(), sevenbysix.s1_adjacency_matrix.toarray())
     assert indexes.tolist() == list(sevenbysix.nodes)
 
 
@@ -1142,7 +1148,9 @@ def test_auxiliary_matrix_on_edges(sevenbysix):
     aux_matrix, indexes = hg.auxiliary_matrix(node=False, index=True)
 
     assert aux_matrix.todense().shape == (len(sevenbysix.edges), len(sevenbysix.edges))
-    assert np.allclose(aux_matrix.A, sevenbysix.s1_edge_adjacency_matrx.A)
+    assert np.allclose(
+        aux_matrix.toarray(), sevenbysix.s1_edge_adjacency_matrix.toarray()
+    )
     assert indexes.tolist() == list(sevenbysix.edges)