[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+    rev: v1.38.0
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yml]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.0a3
     hooks:
       - id: isort
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         exclude: .bumpversion.cfg
@@ -20,30 +20,30 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: v3.1.0
+    rev: v4.0.0
     hooks:
       - id: add-trailing-comma
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
 
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.5.1
     hooks:
       - id: black
         args: ["--safe"]
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38 # v1.7.5
+    rev: v1.7.8 # v1.7.5
     hooks:
       - id: docformatter
         name: Format docstring
         args: [--in-place, --wrap-summaries, "88", --wrap-descriptions, "80", --blank]
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.19
+    rev: 1.0.0
     hooks:
       - id: mdformat
         name: Format markdown

src/obnb/data/annotation/diseases.py

@@ -14,7 +14,8 @@ class DISEASESAnnotation(BaseAnnotationData):
     This is the ``integrated`` disease annotation channel from the Jensen Lab
     DISEASES annotation database, which combines evidences from *text-mining*,
     *knowledge*, and *experiment* channels. See  the
-    `DISEASES <https://diseases.jensenlab.org/About>`_ webpage for more
+    `DISEASES <https://diseases.jensenlab.org/About>`_
+    webpage for more
     information
 
     """

src/obnb/graph/ontology.py

@@ -26,11 +26,11 @@
 class OntologyGraph(DirectedSparseGraph):
     """Ontology graph.
 
-    An ontology graph is a directed acyclic graph (DAG). Here, we represent
-    this data type using DirectedSparseGraph, which keeps track of both the
-    forward direction of edges (``_edge_data``) and the reversed direction of
-    edges (``_rev_edge_data``). This bidirectional awareness is useful in the
-    context of propagating information "upwards" or "downloads".
+    An ontology graph is a directed acyclic graph (DAG). Here, we represent this
+    data type using DirectedSparseGraph, which keeps track of both the forward
+    direction of edges (``_edge_data``) and the reversed direction of edges
+    (``_rev_edge_data``). This bidirectional awareness is useful in the context
+    of propagating information "upwards" or "downloads".
 
     The ``idmap`` attribute is swapped with a more functional ``IDProp`` object
     that allows the storing of node information such as the name and the node

test/test_graph.py

@@ -1079,21 +1079,11 @@ def test_ancestors(self):
         self.assertEqual(graph.ancestors("f"), {"a", "c", "d"})
 
     def test_restrict_to_branch(self):
-        r"""
-
-        a
-        | \
-        b   d
-        |   |     \
-        c   e [z]   f [x, y]
-
-        |
-        V
+        r"""A | \ b   d |   |     \ c   e [z]   f [x, y]
 
-        d
-        |    \
-        e [z]  f [x, y]
+        | V
 
+        d |    \ e [z]  f [x, y]
 
         """
         graph = OntologyGraph()