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

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

.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

@@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behavior, harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
 **Consequence**: A permanent ban from any sort of public interaction within

example/utils.py

@@ -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
 
 

script/release_data.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

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

src/obnb/typing.py → src/obnb/alltypes.py

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

src/obnb/config/__init__.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/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,

src/obnb/data/annotated_ontology/__init__.py

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

src/obnb/data/annotated_ontology/base.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
 
 

src/obnb/data/annotated_ontology/diseases.py

@@ -1,8 +1,8 @@
+from obnb.alltypes import Mapping, Optional, Union
 from obnb.data.annotated_ontology.base import BaseAnnotatedOntologyData
 from obnb.data.annotation import DISEASESAnnotation
 from obnb.data.ontology import MondoDiseaseOntology
 from obnb.label.filters import Compose, LabelsetNonRedFilter, LabelsetRangeFilterSize
-from obnb.typing import Mapping, Optional, Union
 from obnb.util.registers import overload_class
 
 

src/obnb/data/annotated_ontology/disgenet.py

@@ -1,8 +1,8 @@
+from obnb.alltypes import List, Mapping, Optional, Union
 from obnb.data.annotated_ontology.base import BaseAnnotatedOntologyData
 from obnb.data.annotation import DisGeNETAnnotation
 from obnb.data.ontology import MondoDiseaseOntology
 from obnb.label.filters import Compose, LabelsetNonRedFilter, LabelsetRangeFilterSize
-from obnb.typing import List, Mapping, Optional, Union
 from obnb.util.registers import overload_class
 
 

src/obnb/data/annotated_ontology/go.py

@@ -1,8 +1,8 @@
+from obnb.alltypes import List, Mapping, Optional, Union
 from obnb.data.annotated_ontology.base import BaseAnnotatedOntologyData
 from obnb.data.annotation import GeneOntologyAnnotation
 from obnb.data.ontology import GeneOntology
 from obnb.label.filters import Compose, LabelsetNonRedFilter, LabelsetRangeFilterSize
-from obnb.typing import List, Mapping, Optional, Union
 from obnb.util.registers import overload_class
 
 

src/obnb/data/annotated_ontology/hpo.py

@@ -1,8 +1,8 @@
+from obnb.alltypes import List, Mapping, Optional, Union
 from obnb.data.annotated_ontology.base import BaseAnnotatedOntologyData
 from obnb.data.annotation import HumanPhenotypeOntologyAnnotation
 from obnb.data.ontology import MondoDiseaseOntology
 from obnb.label.filters import Compose, LabelsetNonRedFilter, LabelsetRangeFilterSize
-from obnb.typing import List, Mapping, Optional, Union
 
 
 class HPO(BaseAnnotatedOntologyData):

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

src/obnb/data/annotation/base.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import List, Optional, ZipType
 from obnb.data.base import BaseData
-from obnb.typing import List, Optional, ZipType
 from obnb.util.download import download_unzip
 
 

src/obnb/data/annotation/diseases.py

@@ -2,8 +2,8 @@
 
 import pandas as pd
 
+from obnb.alltypes import List, Optional
 from obnb.data.annotation.base import BaseAnnotationData
-from obnb.typing import List, Optional
 
 
 class DISEASESAnnotation(BaseAnnotationData):

src/obnb/data/annotation/disgenet.py

@@ -2,8 +2,8 @@
 
 import pandas as pd
 
+from obnb.alltypes import List, Optional
 from obnb.data.annotation.base import BaseAnnotationData
-from obnb.typing import List, Optional
 
 
 class DisGeNETAnnotation(BaseAnnotationData):

src/obnb/data/annotation/gene_ontology.py

@@ -2,8 +2,8 @@
 
 import pandas as pd
 
+from obnb.alltypes import List, Optional
 from obnb.data.annotation.base import BaseAnnotationData
-from obnb.typing import List, Optional
 
 
 class GeneOntologyAnnotation(BaseAnnotationData):

src/obnb/data/annotation/human_phenotype_ontology.py

@@ -2,8 +2,8 @@
 
 import pandas as pd
 
+from obnb.alltypes import List, Optional
 from obnb.data.annotation.base import BaseAnnotationData
-from obnb.typing import List, Optional
 
 
 class HumanPhenotypeOntologyAnnotation(BaseAnnotationData):

src/obnb/data/base.py

@@ -7,7 +7,7 @@
 import yaml
 
 import obnb
-from obnb.typing import Any, Converter, Dict, List, LogLevel, Mapping, Optional
+from obnb.alltypes import Any, Converter, Dict, List, LogLevel, Mapping, Optional
 from obnb.util.checkers import checkConfig
 from obnb.util.converter import MyGeneInfoConverter
 from obnb.util.download import download_unzip, get_data_url

src/obnb/data/experimental/__init__.py

@@ -8,6 +8,7 @@
     versions of the package.
 
 """
+
 from obnb.data.experimental.alevinfry import AlevinFry
 
 __all__ = [

src/obnb/data/experimental/alevinfry.py

@@ -3,9 +3,9 @@
 except ImportError:
     pyroe = None
 
+from obnb.alltypes import Dict, List, Optional
 from obnb.data.base import BaseData
 from obnb.feature import FeatureVec
-from obnb.typing import Dict, List, Optional
 
 
 class AlevinFry(BaseData, FeatureVec):

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
@@ -13,7 +14,7 @@
 from obnb.data.network.pcnet import PCNet
 from obnb.data.network.proteomehd import ProteomeHD
 from obnb.data.network.signor import SIGNOR
-from obnb.data.network.string import STRING
+from obnb.data.network.stringprot import STRING
 
 __all__ = [
     "BioGRID",

src/obnb/data/network/base.py

@@ -1,8 +1,8 @@
 import ndex2
 
+from obnb.alltypes import Any, Dict, List, Mapping, Optional, Union
 from obnb.data.base import BaseData
 from obnb.graph import SparseGraph
-from obnb.typing import Any, Dict, List, Mapping, Optional, Union
 from obnb.util.download import download_unzip
 from obnb.util.logger import display_pbar
 

src/obnb/data/network/biogrid.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class BioGRID(BaseNDExData):

src/obnb/data/network/bioplex.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class BioPlex(BaseNDExData):

src/obnb/data/network/comppi.py

@@ -3,8 +3,8 @@
 import pandas as pd
 import requests
 
+from obnb.alltypes import Any, Dict, List, Mapping, Optional, Union
 from obnb.data.network.base import BaseURLSparseGraphData
-from obnb.typing import Any, Dict, List, Mapping, Optional, Union
 
 
 class ComPPI(BaseURLSparseGraphData):

src/obnb/data/network/consensuspathdb.py

@@ -4,8 +4,8 @@
 import numpy as np
 import pandas as pd
 
+from obnb.alltypes import List, Literal, Mapping, Optional, Union
 from obnb.data.network.base import BaseURLSparseGraphData
-from obnb.typing import List, Literal, Mapping, Optional, Union
 from obnb.util.download import download_unzip
 
 

src/obnb/data/network/funcoup.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class FunCoup(BaseNDExData):

src/obnb/data/network/hippie.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class HIPPIE(BaseNDExData):

src/obnb/data/network/humanbase.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseURLSparseGraphData
-from obnb.typing import Converter
 
 
 class HumanBaseTopGlobal(BaseURLSparseGraphData):

src/obnb/data/network/humannet.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter, List
 from obnb.data.network.base import BaseURLSparseGraphData
-from obnb.typing import Converter, List
 from obnb.util.registers import overload_class
 
 

src/obnb/data/network/humap.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseURLSparseGraphData
-from obnb.typing import Converter
 
 
 class HuMAP(BaseURLSparseGraphData):

src/obnb/data/network/huri.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class HuRI(BaseNDExData):

src/obnb/data/network/omnipath.py

@@ -3,8 +3,8 @@
 import pandas as pd
 import requests
 
+from obnb.alltypes import List, Mapping, Optional, Union
 from obnb.data.network.base import BaseURLSparseGraphData
-from obnb.typing import List, Mapping, Optional, Union
 from obnb.util.download import stream_download
 
 

src/obnb/data/network/pcnet.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class PCNet(BaseNDExData):

src/obnb/data/network/proteomehd.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class ProteomeHD(BaseNDExData):

src/obnb/data/network/signor.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class SIGNOR(BaseNDExData):

src/obnb/data/network/string.py → src/obnb/data/network/stringprot.py

@@ -1,5 +1,5 @@
+from obnb.alltypes import Converter
 from obnb.data.network.base import BaseNDExData
-from obnb.typing import Converter
 
 
 class STRING(BaseNDExData):

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