[pre-commit.ci] auto fixes from pre-commit.com hooks

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src/nleval/data/network/funcoup.py

@@ -7,8 +7,6 @@ class FunCoup(BaseNDExData):
 
     The edge weights are PFC values, which is a probabilistic estimation about
     whether a pair of genes are functionally coupled.
-
-
     https://funcoup5.scilifelab.se/help/#Citation
 
     """

src/nleval/label/filters/nonred.py

@@ -11,7 +11,8 @@ class LabelsetNonRedFilter(BaseFilter):
     """Filter out redundant labelsets in a labelset collection.
 
     The detailed procedure can be found in the supplementary data of
-    https://doi.org/10.1093/bioinformatics/btaa150 In brief, given a labelset
+    https://doi.org/10.1093/bioinformatics/btaa150
+    In brief, given a labelset
     collection, a graph of labelsets if first constructed based on the
     redundancy score function of interest. Here, we use the combination of
     Jaccard index and overlap coefficient. Then, for each connected component in

test/test_graph.py

@@ -758,7 +758,7 @@ def setUpClass(cls):
         cls.case = test_case1()
 
     def check_graph(self, graph):
-        """compare graph with data, true if identical."""
+        """Compare graph with data, true if identical."""
         mat = self.case.data_mat[:, 1:]
         IDlst = [str(int(i)) for i in self.case.data_mat[:, 0]]
         for idx1, node_id1 in enumerate(IDlst):
@@ -1120,15 +1120,7 @@ def test_restrict_to_branch(self):
         self.assertRaises(IDNotExistError, graph.restrict_to_branch, "g")
 
     def test_read_obo(self):
-        r"""
-
-               a
-        /      |       \
-        b      c (x, y)  d
-        |       \      /
-        e [z]       f
-
-        """
+        r"""A /      |       \ b      c (x, y)  d |       \      / e [z]       f."""
         obo_path = osp.join(SAMPLE_DATA_DIR, "toy_ontology.obo")
         with self.subTest(xref_prefix=None):
             # Do not capture xref when xref_prefix is unset

test/test_label/filters/test_nonred.py

@@ -14,14 +14,10 @@
 def case1():
     r"""Labelset collection test case 1.
 
-    When threshold is set to 0.49, and use overlap (or threshold set to 0.3
-    and use jaccard):
-
-    lb0
-    |   \
-    lb1  lb2
-    |
-    lb3
+    When threshold is set to 0.49, and use overlap (or threshold set to 0.3 and
+    use jaccard):
+
+    lb0 |   \ lb1  lb2 | lb3
 
     The expected outcome is thus: ['lb0', 'lb3']