From 55c93f54b8738b41fa4f14298876c35a7e553962 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 15 Apr 2024 23:14:48 +0000
Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/obnb/__init__.py                         | 1 +
 src/obnb/config/__init__.py                  | 1 +
 src/obnb/data/__init__.py                    | 1 +
 src/obnb/data/annotated_ontology/__init__.py | 1 +
 src/obnb/data/annotation/__init__.py         | 1 +
 src/obnb/data/experimental/__init__.py       | 1 +
 src/obnb/data/network/__init__.py            | 1 +
 src/obnb/data/ontology/__init__.py           | 1 +
 src/obnb/dataset/__init__.py                 | 1 +
 src/obnb/dataset/base.py                     | 1 +
 src/obnb/dataset/dataset.py                  | 1 +
 src/obnb/dataset/dataset_dgl.py              | 1 +
 src/obnb/dataset/dataset_pyg.py              | 1 +
 src/obnb/ext/attnwalk.py                     | 1 +
 src/obnb/ext/orbital_features.py             | 1 +
 src/obnb/feature/__init__.py                 | 1 +
 src/obnb/feature/multifeat.py                | 1 +
 src/obnb/feature/singlefeat.py               | 1 +
 src/obnb/graph/__init__.py                   | 1 +
 src/obnb/label/__init__.py                   | 1 +
 src/obnb/label/filters/__init__.py           | 1 +
 src/obnb/label/split/__init__.py             | 1 +
 src/obnb/metric/__init__.py                  | 1 +
 src/obnb/metric/graphgym_metric.py           | 1 +
 src/obnb/metric/standard.py                  | 1 +
 src/obnb/model_trainer/__init__.py           | 1 +
 src/obnb/registry.py                         | 1 +
 src/obnb/transform/base.py                   | 3 +--
 src/obnb/transform/node_feature.py           | 4 ++--
 src/obnb/typing.py                           | 1 +
 src/obnb/util/checkers.py                    | 1 +
 src/obnb/util/cx_explorer.py                 | 1 +
 src/obnb/util/logger.py                      | 1 +
 src/obnb/util/path.py                        | 1 +
 src/obnb/util/version.py                     | 1 +
 35 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/src/obnb/__init__.py b/src/obnb/__init__.py
index 14702bdf..6a4dc47f 100644
--- a/src/obnb/__init__.py
+++ b/src/obnb/__init__.py
@@ -1,4 +1,5 @@
 """Collection of network learning evaluation utilities."""
+
 from obnb import graph, label, model_trainer
 from obnb.dataset import Dataset, OpenBiomedNetBench
 from obnb.util.checkers import checkVersion
diff --git a/src/obnb/config/__init__.py b/src/obnb/config/__init__.py
index b43fbf65..cf18b0cd 100644
--- a/src/obnb/config/__init__.py
+++ b/src/obnb/config/__init__.py
@@ -1,4 +1,5 @@
 """Configurations used by obnb."""
+
 from obnb.typing import Dict
 
 __all__ = [
diff --git a/src/obnb/data/__init__.py b/src/obnb/data/__init__.py
index 926947e2..dd0e512a 100644
--- a/src/obnb/data/__init__.py
+++ b/src/obnb/data/__init__.py
@@ -1,4 +1,5 @@
 """Interface with various databases to retrieve data."""
+
 from obnb.data import annotated_ontology, annotation, network, ontology
 from obnb.data.annotated_ontology import (
     DISEASES,
diff --git a/src/obnb/data/annotated_ontology/__init__.py b/src/obnb/data/annotated_ontology/__init__.py
index 2ebbf6c4..e8905502 100644
--- a/src/obnb/data/annotated_ontology/__init__.py
+++ b/src/obnb/data/annotated_ontology/__init__.py
@@ -1,4 +1,5 @@
 """Annotated ontology data."""
+
 from obnb.data.annotated_ontology.diseases import (
     DISEASES,
     DISEASES_ExperimentsFiltered,
diff --git a/src/obnb/data/annotation/__init__.py b/src/obnb/data/annotation/__init__.py
index ab2956c6..76ed4807 100644
--- a/src/obnb/data/annotation/__init__.py
+++ b/src/obnb/data/annotation/__init__.py
@@ -1,4 +1,5 @@
 """Annotation data."""
+
 from obnb.data.annotation.diseases import DISEASESAnnotation
 from obnb.data.annotation.disgenet import DisGeNETAnnotation
 from obnb.data.annotation.gene_ontology import GeneOntologyAnnotation
diff --git a/src/obnb/data/experimental/__init__.py b/src/obnb/data/experimental/__init__.py
index 88ac3765..cb241081 100644
--- a/src/obnb/data/experimental/__init__.py
+++ b/src/obnb/data/experimental/__init__.py
@@ -8,6 +8,7 @@
     versions of the package.
 
 """
+
 from obnb.data.experimental.alevinfry import AlevinFry
 
 __all__ = [
diff --git a/src/obnb/data/network/__init__.py b/src/obnb/data/network/__init__.py
index 343999eb..72c3fd22 100644
--- a/src/obnb/data/network/__init__.py
+++ b/src/obnb/data/network/__init__.py
@@ -1,4 +1,5 @@
 """Network data."""
+
 from obnb.data.network.biogrid import BioGRID
 from obnb.data.network.bioplex import BioPlex
 from obnb.data.network.comppi import ComPPIHumanInt
diff --git a/src/obnb/data/ontology/__init__.py b/src/obnb/data/ontology/__init__.py
index 0190bef6..44fa3376 100644
--- a/src/obnb/data/ontology/__init__.py
+++ b/src/obnb/data/ontology/__init__.py
@@ -1,4 +1,5 @@
 """Ontology data."""
+
 from obnb.data.ontology.gene_ontology import GeneOntology
 from obnb.data.ontology.mondo import MondoDiseaseOntology
 
diff --git a/src/obnb/dataset/__init__.py b/src/obnb/dataset/__init__.py
index e8e14079..fe9727b3 100644
--- a/src/obnb/dataset/__init__.py
+++ b/src/obnb/dataset/__init__.py
@@ -1,4 +1,5 @@
 """Dataset objects."""
+
 from obnb.dataset.base import Dataset
 from obnb.dataset.dataset import OpenBiomedNetBench
 from obnb.dataset.dataset_dgl import OpenBiomedNetBenchDGL
diff --git a/src/obnb/dataset/base.py b/src/obnb/dataset/base.py
index 39eddfee..1bf4f1d7 100644
--- a/src/obnb/dataset/base.py
+++ b/src/obnb/dataset/base.py
@@ -1,4 +1,5 @@
 """Dataset object."""
+
 import numpy as np
 from sklearn.preprocessing import KBinsDiscretizer
 
diff --git a/src/obnb/dataset/dataset.py b/src/obnb/dataset/dataset.py
index 660e8448..c72dc83a 100644
--- a/src/obnb/dataset/dataset.py
+++ b/src/obnb/dataset/dataset.py
@@ -1,4 +1,5 @@
 """Helper functions to construct processed datasets."""
+
 import obnb.data
 import obnb.label.split
 from obnb.dataset.base import Dataset
diff --git a/src/obnb/dataset/dataset_dgl.py b/src/obnb/dataset/dataset_dgl.py
index 6e904812..7e7a53f1 100644
--- a/src/obnb/dataset/dataset_dgl.py
+++ b/src/obnb/dataset/dataset_dgl.py
@@ -1,4 +1,5 @@
 """DGL dataset object."""
+
 import os.path as osp
 
 try:
diff --git a/src/obnb/dataset/dataset_pyg.py b/src/obnb/dataset/dataset_pyg.py
index fb3aee91..a3071563 100644
--- a/src/obnb/dataset/dataset_pyg.py
+++ b/src/obnb/dataset/dataset_pyg.py
@@ -1,4 +1,5 @@
 """PyTorch Geometric dataset object."""
+
 import os.path as osp
 
 try:
diff --git a/src/obnb/ext/attnwalk.py b/src/obnb/ext/attnwalk.py
index 76f7793f..a965e68d 100644
--- a/src/obnb/ext/attnwalk.py
+++ b/src/obnb/ext/attnwalk.py
@@ -11,6 +11,7 @@
 }
 
 """
+
 from typing import Union
 
 import networkx as nx
diff --git a/src/obnb/ext/orbital_features.py b/src/obnb/ext/orbital_features.py
index 743a6aa9..0b0de04d 100644
--- a/src/obnb/ext/orbital_features.py
+++ b/src/obnb/ext/orbital_features.py
@@ -1,4 +1,5 @@
 """Grpahlet orbital feature extraction."""
+
 import itertools
 import multiprocessing
 from functools import partial
diff --git a/src/obnb/feature/__init__.py b/src/obnb/feature/__init__.py
index 15e3855a..1820407e 100644
--- a/src/obnb/feature/__init__.py
+++ b/src/obnb/feature/__init__.py
@@ -1,4 +1,5 @@
 """Feature objects."""
+
 from obnb.feature.multifeat import MultiFeatureVec
 from obnb.feature.singlefeat import FeatureVec
 
diff --git a/src/obnb/feature/multifeat.py b/src/obnb/feature/multifeat.py
index 58e40aae..29bec19c 100644
--- a/src/obnb/feature/multifeat.py
+++ b/src/obnb/feature/multifeat.py
@@ -1,4 +1,5 @@
 """Multi modality feature objects."""
+
 from itertools import chain
 
 import numpy as np
diff --git a/src/obnb/feature/singlefeat.py b/src/obnb/feature/singlefeat.py
index 42907dba..7a7d3f74 100644
--- a/src/obnb/feature/singlefeat.py
+++ b/src/obnb/feature/singlefeat.py
@@ -1,4 +1,5 @@
 """Single modality feature objects."""
+
 import numpy as np
 
 from obnb.feature.base import BaseFeature
diff --git a/src/obnb/graph/__init__.py b/src/obnb/graph/__init__.py
index 370a32be..378b3f03 100644
--- a/src/obnb/graph/__init__.py
+++ b/src/obnb/graph/__init__.py
@@ -1,4 +1,5 @@
 """Graph and feature vector objects."""
+
 from obnb.graph.dense import DenseGraph
 from obnb.graph.ontology import OntologyGraph
 from obnb.graph.sparse import DirectedSparseGraph, SparseGraph
diff --git a/src/obnb/label/__init__.py b/src/obnb/label/__init__.py
index 8950654a..c4f25195 100644
--- a/src/obnb/label/__init__.py
+++ b/src/obnb/label/__init__.py
@@ -1,4 +1,5 @@
 """Labelset collection with splitting and filtering utilities."""
+
 from obnb.label import filters, split
 from obnb.label.collection import LabelsetCollection
 
diff --git a/src/obnb/label/filters/__init__.py b/src/obnb/label/filters/__init__.py
index 9329b110..b5689547 100644
--- a/src/obnb/label/filters/__init__.py
+++ b/src/obnb/label/filters/__init__.py
@@ -1,4 +1,5 @@
 """Filter objecst for preprocessing the labelset collection."""
+
 from obnb.label.filters.base import Compose
 from obnb.label.filters.existence_filter import (
     EntityExistenceFilter,
diff --git a/src/obnb/label/split/__init__.py b/src/obnb/label/split/__init__.py
index 2657e2ea..204e5dc8 100644
--- a/src/obnb/label/split/__init__.py
+++ b/src/obnb/label/split/__init__.py
@@ -1,4 +1,5 @@
 """Genearting data splits from the labelset collection."""
+
 from obnb.label.split.holdout import (
     AllHoldout,
     RandomRatioHoldout,
diff --git a/src/obnb/metric/__init__.py b/src/obnb/metric/__init__.py
index 3db2080f..be2f4c9b 100644
--- a/src/obnb/metric/__init__.py
+++ b/src/obnb/metric/__init__.py
@@ -1,4 +1,5 @@
 """Metric functions used for evaluation."""
+
 from obnb.metric.standard import auroc, log2_auprc_prior, precision_at_topk
 
 __all__ = [
diff --git a/src/obnb/metric/graphgym_metric.py b/src/obnb/metric/graphgym_metric.py
index 1578ee5c..d03af384 100644
--- a/src/obnb/metric/graphgym_metric.py
+++ b/src/obnb/metric/graphgym_metric.py
@@ -1,4 +1,5 @@
 """Custom metrics compatible with GraphGym logger."""
+
 from functools import wraps
 
 import torch
diff --git a/src/obnb/metric/standard.py b/src/obnb/metric/standard.py
index 070344c2..5e6acb55 100644
--- a/src/obnb/metric/standard.py
+++ b/src/obnb/metric/standard.py
@@ -1,4 +1,5 @@
 """Standard metric extending those available in sklearn."""
+
 from functools import wraps
 
 try:
diff --git a/src/obnb/model_trainer/__init__.py b/src/obnb/model_trainer/__init__.py
index 86840734..593cc912 100644
--- a/src/obnb/model_trainer/__init__.py
+++ b/src/obnb/model_trainer/__init__.py
@@ -1,4 +1,5 @@
 """Unified framework for training different types of models."""
+
 from obnb.model_trainer.label_propagation import LabelPropagationTrainer
 from obnb.model_trainer.supervised_learning import (
     MultiSupervisedLearningTrainer,
diff --git a/src/obnb/registry.py b/src/obnb/registry.py
index 8f84bef4..d3c95362 100644
--- a/src/obnb/registry.py
+++ b/src/obnb/registry.py
@@ -3,6 +3,7 @@
 Helps interface with user defined modules for OBNB pipelines.
 
 """
+
 from obnb.typing import Any
 from obnb.util.misc import DotDict
 
diff --git a/src/obnb/transform/base.py b/src/obnb/transform/base.py
index 30be8d8f..1fa2a061 100644
--- a/src/obnb/transform/base.py
+++ b/src/obnb/transform/base.py
@@ -33,5 +33,4 @@ def fullname(self) -> str:
 
 class BaseDatasetTransform(BaseTransform, ABC):
     @abstractmethod
-    def __call__(self, dataset):
-        ...
+    def __call__(self, dataset): ...
diff --git a/src/obnb/transform/node_feature.py b/src/obnb/transform/node_feature.py
index 6ddc4d02..1d7f82e8 100644
--- a/src/obnb/transform/node_feature.py
+++ b/src/obnb/transform/node_feature.py
@@ -1,4 +1,5 @@
 """Node feature transformation module."""
+
 import warnings
 from abc import ABC, abstractmethod
 
@@ -50,8 +51,7 @@ def __call__(self, dataset):
             dataset.feature = FeatureVec.from_mat(feat, node_ids)
 
     @abstractmethod
-    def _prepare_feat(self, dataset) -> np.ndarray:
-        ...
+    def _prepare_feat(self, dataset) -> np.ndarray: ...
 
 
 @register_nodefeat
diff --git a/src/obnb/typing.py b/src/obnb/typing.py
index 432a8a3f..bf81068b 100644
--- a/src/obnb/typing.py
+++ b/src/obnb/typing.py
@@ -1,4 +1,5 @@
 """Collection of types used in obnb."""
+
 from typing import (
     Any,
     Callable,
diff --git a/src/obnb/util/checkers.py b/src/obnb/util/checkers.py
index 81fbf4b2..f2ae1872 100755
--- a/src/obnb/util/checkers.py
+++ b/src/obnb/util/checkers.py
@@ -4,6 +4,7 @@
 a function call is valid.
 
 """
+
 import os
 import warnings
 from typing import get_args
diff --git a/src/obnb/util/cx_explorer.py b/src/obnb/util/cx_explorer.py
index f6f24a3b..2aee4651 100644
--- a/src/obnb/util/cx_explorer.py
+++ b/src/obnb/util/cx_explorer.py
@@ -1,4 +1,5 @@
 """Utility for exploring NDEx CX data."""
+
 import itertools
 import json
 from collections import defaultdict
diff --git a/src/obnb/util/logger.py b/src/obnb/util/logger.py
index ebc0dc7e..3d4888e1 100644
--- a/src/obnb/util/logger.py
+++ b/src/obnb/util/logger.py
@@ -1,4 +1,5 @@
 """Logger utils."""
+
 import logging
 import logging.config
 import os
diff --git a/src/obnb/util/path.py b/src/obnb/util/path.py
index 878b9d61..4cd8e988 100644
--- a/src/obnb/util/path.py
+++ b/src/obnb/util/path.py
@@ -1,4 +1,5 @@
 """Path utilities."""
+
 import hashlib
 import os.path as osp
 
diff --git a/src/obnb/util/version.py b/src/obnb/util/version.py
index 83d1ce15..a31761a3 100644
--- a/src/obnb/util/version.py
+++ b/src/obnb/util/version.py
@@ -1,4 +1,5 @@
 """Version utility module for obnb."""
+
 from obnb import config
 from obnb.typing import List