Merge pull request #502 from falquaddoomi/general-testing-fixes

Fixes various test, pre-commit issues after fixing testing workflow

Author: falquaddoomi

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yml]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: .bumpversion.cfg
@@ -25,25 +25,25 @@ repos:
       - id: add-trailing-comma
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
 
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.10.0
     hooks:
       - id: black
         args: ["--safe"]
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38 # 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: 0.7.17
+    rev: 0.7.19
     hooks:
       - id: mdformat
         name: Format markdown

CODE_OF_CONDUCT.md

@@ -1,4 +1,5 @@
 import obnb.data
+from obnb.alltypes import LogLevel
 from obnb.label.filters import (
     Compose,
     EntityExistenceFilter,
@@ -7,7 +8,6 @@
     NegativeGeneratorHypergeom,
 )
 from obnb.label.split import RatioPartition
-from obnb.typing import LogLevel
 from obnb.util.converter import GenePropertyConverter
 
 

example/utils.py

@@ -13,9 +13,9 @@
 
 import obnb.data
 from obnb import logger
+from obnb.alltypes import Dict, List, Tuple
 from obnb.config import OBNB_DATA_URL_DICT
 from obnb.data.base import BaseData
-from obnb.typing import Dict, List, Tuple
 from obnb.util.converter import GenePropertyConverter
 
 HOMEDIR = Path(__file__).resolve().parent

script/release_data.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

src/obnb/__init__.py

@@ -1,4 +1,5 @@
 """Collection of types used in obnb."""
+
 from typing import (
     Any,
     Callable,

src/obnb/typing.py src/obnb/alltypes.pysrc/obnb/typing.py renamed to src/obnb/alltypes.py

@@ -1,5 +1,6 @@
 """Configurations used by obnb."""
-from obnb.typing import Dict
+
+from obnb.alltypes import Dict
 
 __all__ = [
     "DEFAULT_RETRY_DELAY",

src/obnb/config/__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,

src/obnb/data/__init__.py

@@ -1,4 +1,5 @@
 """Annotated ontology data."""
+
 from obnb.data.annotated_ontology.diseases import (
     DISEASES,
     DISEASES_ExperimentsFiltered,

src/obnb/data/annotated_ontology/__init__.py

@@ -1,11 +1,11 @@
 from tqdm import tqdm
 
+from obnb.alltypes import Any, Dict, List, Optional, Type
 from obnb.data.annotation.base import BaseAnnotationData
 from obnb.data.base import BaseData
 from obnb.data.ontology.base import BaseOntologyData
 from obnb.exception import IDNotExistError
 from obnb.label import LabelsetCollection
-from obnb.typing import Any, Dict, List, Optional, Type
 from obnb.util.logger import display_pbar