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

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

script/release_data.py

@@ -28,7 +28,8 @@
 LABEL_DATA = sorted(obnb.data.annotated_ontology.__all__)
 DATA_RELEASE_VERSION = obnb.__data_version__
 
-REPORT_TEMPLATE = r"""## Overview
+REPORT_TEMPLATE =\
+                  r"""## Overview
 
 - Release version: {{ version }}
 - Release date: {{ time }}

src/obnb/exception.py

@@ -1,26 +1,19 @@
 class DataNotFoundError(Exception):
     """Raised when an particular version of arvhival data is unavailable."""
 
-
 class ExceededMaxNumRetries(Exception):
     """Raised when the number of download retries exceeds the limit."""
 
-
 class IDNotExistError(Exception):
     """Raised when query ID not exist."""
 
-
 class IDExistsError(Exception):
     """Raised when try to add new ID that already exists."""
-
-
 class EdgeNotExistError(Exception):
     """Raised when the edge being accessed does not exist."""
-
-
 class NotConvergedWarning(RuntimeWarning):
     """Warn when model not converged."""
 
-
 class OboTermIncompleteError(Exception):
     """Raised when the obo term do not have an ID or a name."""
+

src/obnb/ext/__init__.py

@@ -1 +1,2 @@
 """Extension modules to interface with obnb."""
+

src/obnb/label/filters/range_filter.py

@@ -161,6 +161,7 @@ def get_val_getter(self, lsc):
 
         """
 
+
         def val_getter(label_id):
             y_all, masks = lsc.split(self.splitter, **self.kwargs)
             neg_idx = lsc.entity[lsc.get_negative(label_id)]

src/obnb/model/__init__.py

@@ -1 +1,2 @@
 """Collection of network based prediction models."""
+

src/obnb/transform/__init__.py

@@ -1 +1,2 @@
 """Transformation module."""
+

src/obnb/util/deprecated.py

@@ -23,6 +23,7 @@ def __init__(
     def __call__(self, func):
         """Wraps the function with deprecation warning."""
 
+
         @wraps(func)
         def wrapped(*args, **kwargs):
             warnings.simplefilter("always", self.category)

src/obnb/util/parallel.py

@@ -81,6 +81,7 @@ def __init__(
     def __call__(self, func):
         """Return the parallelized function over the input arguments."""
 
+
         def wrapper(*func_args, **func_kwargs):
             n_workers = self.n_workers
             n_jobs = self.n_jobs
@@ -236,6 +237,7 @@ class ParDatMap(ParDat):
     def __call__(self, func):
         """Return the parallelized function over the input arguments."""
 
+
         def wrapper(*func_args, **func_kwargs):
             n_workers = self.n_workers
             n_jobs = self.n_jobs
@@ -283,6 +285,7 @@ class ParDatExe(ParDat):
     def __call__(self, func):
         """Return the parallelized function over the input arguments."""
 
+
         def wrapper(*func_args, **func_kwargs):
             n_workers = self.n_workers
             n_jobs = self.n_jobs

src/obnb/util/timer.py

@@ -19,6 +19,7 @@ def __init__(self, verbose: bool = True) -> None:
     def __call__(self, func):
         """Return function wrapped with timer."""
 
+
         def wrapper(*args):
             start = time.perf_counter()
             func(*args)

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()