From f0bfc1e2caad7673e555633cb5f8600f75c0d5c6 Mon Sep 17 00:00:00 2001 From: Faisal Alquaddoomi Date: Wed, 4 Dec 2024 10:40:18 -0700 Subject: [PATCH 1/4] Fixed builtin module shadowing: obnb.typing became obnb.alltypes, obnb.data.network.string became .stringprot --- example/utils.py | 2 +- script/release_data.py | 2 +- src/obnb/{typing.py => alltypes.py} | 0 src/obnb/config/__init__.py | 2 +- src/obnb/data/annotated_ontology/base.py | 2 +- src/obnb/data/annotated_ontology/diseases.py | 2 +- src/obnb/data/annotated_ontology/disgenet.py | 2 +- src/obnb/data/annotated_ontology/go.py | 2 +- src/obnb/data/annotated_ontology/hpo.py | 2 +- src/obnb/data/annotation/base.py | 2 +- src/obnb/data/annotation/diseases.py | 2 +- src/obnb/data/annotation/disgenet.py | 2 +- src/obnb/data/annotation/gene_ontology.py | 2 +- src/obnb/data/annotation/human_phenotype_ontology.py | 2 +- src/obnb/data/base.py | 2 +- src/obnb/data/experimental/alevinfry.py | 2 +- src/obnb/data/network/__init__.py | 2 +- src/obnb/data/network/base.py | 2 +- src/obnb/data/network/biogrid.py | 2 +- src/obnb/data/network/bioplex.py | 2 +- src/obnb/data/network/comppi.py | 2 +- src/obnb/data/network/consensuspathdb.py | 2 +- src/obnb/data/network/funcoup.py | 2 +- src/obnb/data/network/hippie.py | 2 +- src/obnb/data/network/humanbase.py | 2 +- src/obnb/data/network/humannet.py | 2 +- src/obnb/data/network/humap.py | 2 +- src/obnb/data/network/huri.py | 2 +- src/obnb/data/network/omnipath.py | 2 +- src/obnb/data/network/pcnet.py | 2 +- src/obnb/data/network/proteomehd.py | 2 +- src/obnb/data/network/signor.py | 2 +- src/obnb/data/network/{string.py => stringprot.py} | 2 +- src/obnb/data/ontology/base.py | 2 +- src/obnb/dataset/base.py | 2 +- src/obnb/dataset/dataset.py | 2 +- src/obnb/dataset/dataset_dgl.py | 2 +- src/obnb/dataset/dataset_pyg.py | 2 +- src/obnb/ext/grape.py | 2 +- src/obnb/ext/orbital_features.py | 2 +- src/obnb/ext/pecanpy.py | 2 +- src/obnb/ext/sknetwork.py | 2 +- src/obnb/feature/base.py | 2 +- src/obnb/feature/multifeat.py | 2 +- src/obnb/feature/singlefeat.py | 2 +- src/obnb/graph/base.py | 2 +- src/obnb/graph/dense.py | 2 +- src/obnb/graph/ontology.py | 2 +- src/obnb/graph/sparse.py | 2 +- src/obnb/label/collection.py | 2 +- src/obnb/label/filters/base.py | 2 +- src/obnb/label/filters/existence_filter.py | 2 +- src/obnb/label/filters/negative_generator.py | 2 +- src/obnb/label/filters/nonred.py | 2 +- src/obnb/label/filters/pairwise_filter.py | 2 +- src/obnb/label/filters/range_filter.py | 2 +- src/obnb/label/filters/value_filter.py | 2 +- src/obnb/label/split/base.py | 2 +- src/obnb/label/split/holdout.py | 2 +- src/obnb/label/split/partition.py | 2 +- src/obnb/metric/graphgym_metric.py | 2 +- src/obnb/metric/standard.py | 2 +- src/obnb/model_trainer/base.py | 2 +- src/obnb/model_trainer/gnn.py | 2 +- src/obnb/model_trainer/graphgym.py | 2 +- src/obnb/model_trainer/label_propagation.py | 2 +- src/obnb/model_trainer/supervised_learning.py | 2 +- src/obnb/registry.py | 2 +- src/obnb/transform/base.py | 2 +- src/obnb/transform/node_feature.py | 2 +- src/obnb/util/checkers.py | 2 +- src/obnb/util/converter.py | 2 +- src/obnb/util/cx_explorer.py | 2 +- src/obnb/util/download.py | 2 +- src/obnb/util/idhandler.py | 2 +- src/obnb/util/logger.py | 2 +- src/obnb/util/misc.py | 2 +- src/obnb/util/parallel.py | 2 +- src/obnb/util/registers.py | 2 +- src/obnb/util/resolver.py | 2 +- src/obnb/util/version.py | 2 +- test/test_util/test_checkers.py | 2 +- test/util/checkers/test_check_values.py | 2 +- 83 files changed, 82 insertions(+), 82 deletions(-) rename src/obnb/{typing.py => alltypes.py} (100%) rename src/obnb/data/network/{string.py => stringprot.py} (96%) diff --git a/example/utils.py b/example/utils.py index 73f0dae1..4a12945b 100644 --- a/example/utils.py +++ b/example/utils.py @@ -7,7 +7,7 @@ NegativeGeneratorHypergeom, ) from obnb.label.split import RatioPartition -from obnb.typing import LogLevel +from obnb.alltypes import LogLevel from obnb.util.converter import GenePropertyConverter diff --git a/script/release_data.py b/script/release_data.py index 4585caae..bdd2433a 100644 --- a/script/release_data.py +++ b/script/release_data.py @@ -15,7 +15,7 @@ from obnb import logger from obnb.config import OBNB_DATA_URL_DICT from obnb.data.base import BaseData -from obnb.typing import Dict, List, Tuple +from obnb.alltypes import Dict, List, Tuple from obnb.util.converter import GenePropertyConverter HOMEDIR = Path(__file__).resolve().parent diff --git a/src/obnb/typing.py b/src/obnb/alltypes.py similarity index 100% rename from src/obnb/typing.py rename to src/obnb/alltypes.py diff --git a/src/obnb/config/__init__.py b/src/obnb/config/__init__.py index b43fbf65..4081f823 100644 --- a/src/obnb/config/__init__.py +++ b/src/obnb/config/__init__.py @@ -1,5 +1,5 @@ """Configurations used by obnb.""" -from obnb.typing import Dict +from obnb.alltypes import Dict __all__ = [ "DEFAULT_RETRY_DELAY", diff --git a/src/obnb/data/annotated_ontology/base.py b/src/obnb/data/annotated_ontology/base.py index a57e5b0a..cd0d25be 100644 --- a/src/obnb/data/annotated_ontology/base.py +++ b/src/obnb/data/annotated_ontology/base.py @@ -5,7 +5,7 @@ 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.alltypes import Any, Dict, List, Optional, Type from obnb.util.logger import display_pbar diff --git a/src/obnb/data/annotated_ontology/diseases.py b/src/obnb/data/annotated_ontology/diseases.py index 65663c5c..c0f8dd6d 100644 --- a/src/obnb/data/annotated_ontology/diseases.py +++ b/src/obnb/data/annotated_ontology/diseases.py @@ -2,7 +2,7 @@ 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.alltypes import Mapping, Optional, Union from obnb.util.registers import overload_class diff --git a/src/obnb/data/annotated_ontology/disgenet.py b/src/obnb/data/annotated_ontology/disgenet.py index c842f5ff..0d765a0c 100644 --- a/src/obnb/data/annotated_ontology/disgenet.py +++ b/src/obnb/data/annotated_ontology/disgenet.py @@ -2,7 +2,7 @@ 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.alltypes import List, Mapping, Optional, Union from obnb.util.registers import overload_class diff --git a/src/obnb/data/annotated_ontology/go.py b/src/obnb/data/annotated_ontology/go.py index 1a7d4655..e621d0f6 100644 --- a/src/obnb/data/annotated_ontology/go.py +++ b/src/obnb/data/annotated_ontology/go.py @@ -2,7 +2,7 @@ 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.alltypes import List, Mapping, Optional, Union from obnb.util.registers import overload_class diff --git a/src/obnb/data/annotated_ontology/hpo.py b/src/obnb/data/annotated_ontology/hpo.py index d66ae187..fb027d66 100644 --- a/src/obnb/data/annotated_ontology/hpo.py +++ b/src/obnb/data/annotated_ontology/hpo.py @@ -2,7 +2,7 @@ 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 +from obnb.alltypes import List, Mapping, Optional, Union class HPO(BaseAnnotatedOntologyData): diff --git a/src/obnb/data/annotation/base.py b/src/obnb/data/annotation/base.py index e52e25aa..39ef1202 100644 --- a/src/obnb/data/annotation/base.py +++ b/src/obnb/data/annotation/base.py @@ -1,5 +1,5 @@ from obnb.data.base import BaseData -from obnb.typing import List, Optional, ZipType +from obnb.alltypes import List, Optional, ZipType from obnb.util.download import download_unzip diff --git a/src/obnb/data/annotation/diseases.py b/src/obnb/data/annotation/diseases.py index 7c93775c..a626f331 100644 --- a/src/obnb/data/annotation/diseases.py +++ b/src/obnb/data/annotation/diseases.py @@ -3,7 +3,7 @@ import pandas as pd from obnb.data.annotation.base import BaseAnnotationData -from obnb.typing import List, Optional +from obnb.alltypes import List, Optional class DISEASESAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/annotation/disgenet.py b/src/obnb/data/annotation/disgenet.py index 84ce2bff..e7e74945 100644 --- a/src/obnb/data/annotation/disgenet.py +++ b/src/obnb/data/annotation/disgenet.py @@ -3,7 +3,7 @@ import pandas as pd from obnb.data.annotation.base import BaseAnnotationData -from obnb.typing import List, Optional +from obnb.alltypes import List, Optional class DisGeNETAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/annotation/gene_ontology.py b/src/obnb/data/annotation/gene_ontology.py index 826fab9c..a98f3f15 100644 --- a/src/obnb/data/annotation/gene_ontology.py +++ b/src/obnb/data/annotation/gene_ontology.py @@ -3,7 +3,7 @@ import pandas as pd from obnb.data.annotation.base import BaseAnnotationData -from obnb.typing import List, Optional +from obnb.alltypes import List, Optional class GeneOntologyAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/annotation/human_phenotype_ontology.py b/src/obnb/data/annotation/human_phenotype_ontology.py index c4404589..5360b7be 100644 --- a/src/obnb/data/annotation/human_phenotype_ontology.py +++ b/src/obnb/data/annotation/human_phenotype_ontology.py @@ -3,7 +3,7 @@ import pandas as pd from obnb.data.annotation.base import BaseAnnotationData -from obnb.typing import List, Optional +from obnb.alltypes import List, Optional class HumanPhenotypeOntologyAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/base.py b/src/obnb/data/base.py index d4767534..8122a3b9 100644 --- a/src/obnb/data/base.py +++ b/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 diff --git a/src/obnb/data/experimental/alevinfry.py b/src/obnb/data/experimental/alevinfry.py index ae672377..f5f41a0e 100644 --- a/src/obnb/data/experimental/alevinfry.py +++ b/src/obnb/data/experimental/alevinfry.py @@ -5,7 +5,7 @@ from obnb.data.base import BaseData from obnb.feature import FeatureVec -from obnb.typing import Dict, List, Optional +from obnb.alltypes import Dict, List, Optional class AlevinFry(BaseData, FeatureVec): diff --git a/src/obnb/data/network/__init__.py b/src/obnb/data/network/__init__.py index 343999eb..fa842e22 100644 --- a/src/obnb/data/network/__init__.py +++ b/src/obnb/data/network/__init__.py @@ -13,7 +13,7 @@ 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", diff --git a/src/obnb/data/network/base.py b/src/obnb/data/network/base.py index 6b2d4a0d..d2f02af4 100644 --- a/src/obnb/data/network/base.py +++ b/src/obnb/data/network/base.py @@ -2,7 +2,7 @@ from obnb.data.base import BaseData from obnb.graph import SparseGraph -from obnb.typing import Any, Dict, List, Mapping, Optional, Union +from obnb.alltypes import Any, Dict, List, Mapping, Optional, Union from obnb.util.download import download_unzip from obnb.util.logger import display_pbar diff --git a/src/obnb/data/network/biogrid.py b/src/obnb/data/network/biogrid.py index 03b0cb0c..3d8536b8 100644 --- a/src/obnb/data/network/biogrid.py +++ b/src/obnb/data/network/biogrid.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class BioGRID(BaseNDExData): diff --git a/src/obnb/data/network/bioplex.py b/src/obnb/data/network/bioplex.py index df173305..9b796e46 100644 --- a/src/obnb/data/network/bioplex.py +++ b/src/obnb/data/network/bioplex.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class BioPlex(BaseNDExData): diff --git a/src/obnb/data/network/comppi.py b/src/obnb/data/network/comppi.py index 31640dc5..ef5943b7 100644 --- a/src/obnb/data/network/comppi.py +++ b/src/obnb/data/network/comppi.py @@ -4,7 +4,7 @@ import requests from obnb.data.network.base import BaseURLSparseGraphData -from obnb.typing import Any, Dict, List, Mapping, Optional, Union +from obnb.alltypes import Any, Dict, List, Mapping, Optional, Union class ComPPI(BaseURLSparseGraphData): diff --git a/src/obnb/data/network/consensuspathdb.py b/src/obnb/data/network/consensuspathdb.py index ad358764..f658ae5d 100644 --- a/src/obnb/data/network/consensuspathdb.py +++ b/src/obnb/data/network/consensuspathdb.py @@ -5,7 +5,7 @@ import pandas as pd from obnb.data.network.base import BaseURLSparseGraphData -from obnb.typing import List, Literal, Mapping, Optional, Union +from obnb.alltypes import List, Literal, Mapping, Optional, Union from obnb.util.download import download_unzip diff --git a/src/obnb/data/network/funcoup.py b/src/obnb/data/network/funcoup.py index 24c464ce..c7aaa82e 100644 --- a/src/obnb/data/network/funcoup.py +++ b/src/obnb/data/network/funcoup.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class FunCoup(BaseNDExData): diff --git a/src/obnb/data/network/hippie.py b/src/obnb/data/network/hippie.py index 24c719d8..696b4851 100644 --- a/src/obnb/data/network/hippie.py +++ b/src/obnb/data/network/hippie.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class HIPPIE(BaseNDExData): diff --git a/src/obnb/data/network/humanbase.py b/src/obnb/data/network/humanbase.py index baa17cf0..8a0d6a9c 100644 --- a/src/obnb/data/network/humanbase.py +++ b/src/obnb/data/network/humanbase.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseURLSparseGraphData -from obnb.typing import Converter +from obnb.alltypes import Converter class HumanBaseTopGlobal(BaseURLSparseGraphData): diff --git a/src/obnb/data/network/humannet.py b/src/obnb/data/network/humannet.py index d9690e10..020aa6bb 100644 --- a/src/obnb/data/network/humannet.py +++ b/src/obnb/data/network/humannet.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseURLSparseGraphData -from obnb.typing import Converter, List +from obnb.alltypes import Converter, List from obnb.util.registers import overload_class diff --git a/src/obnb/data/network/humap.py b/src/obnb/data/network/humap.py index c4337945..44671bf1 100644 --- a/src/obnb/data/network/humap.py +++ b/src/obnb/data/network/humap.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseURLSparseGraphData -from obnb.typing import Converter +from obnb.alltypes import Converter class HuMAP(BaseURLSparseGraphData): diff --git a/src/obnb/data/network/huri.py b/src/obnb/data/network/huri.py index 39e7ce5f..5feee3df 100644 --- a/src/obnb/data/network/huri.py +++ b/src/obnb/data/network/huri.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class HuRI(BaseNDExData): diff --git a/src/obnb/data/network/omnipath.py b/src/obnb/data/network/omnipath.py index 9ecaceb1..d20d34ff 100644 --- a/src/obnb/data/network/omnipath.py +++ b/src/obnb/data/network/omnipath.py @@ -4,7 +4,7 @@ import requests from obnb.data.network.base import BaseURLSparseGraphData -from obnb.typing import List, Mapping, Optional, Union +from obnb.alltypes import List, Mapping, Optional, Union from obnb.util.download import stream_download diff --git a/src/obnb/data/network/pcnet.py b/src/obnb/data/network/pcnet.py index 220de99e..cc5cbf75 100644 --- a/src/obnb/data/network/pcnet.py +++ b/src/obnb/data/network/pcnet.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class PCNet(BaseNDExData): diff --git a/src/obnb/data/network/proteomehd.py b/src/obnb/data/network/proteomehd.py index 9f238f91..acc7740d 100644 --- a/src/obnb/data/network/proteomehd.py +++ b/src/obnb/data/network/proteomehd.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class ProteomeHD(BaseNDExData): diff --git a/src/obnb/data/network/signor.py b/src/obnb/data/network/signor.py index 83a9f00a..acdc72c8 100644 --- a/src/obnb/data/network/signor.py +++ b/src/obnb/data/network/signor.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class SIGNOR(BaseNDExData): diff --git a/src/obnb/data/network/string.py b/src/obnb/data/network/stringprot.py similarity index 96% rename from src/obnb/data/network/string.py rename to src/obnb/data/network/stringprot.py index 4c356270..f3989a4e 100644 --- a/src/obnb/data/network/string.py +++ b/src/obnb/data/network/stringprot.py @@ -1,5 +1,5 @@ from obnb.data.network.base import BaseNDExData -from obnb.typing import Converter +from obnb.alltypes import Converter class STRING(BaseNDExData): diff --git a/src/obnb/data/ontology/base.py b/src/obnb/data/ontology/base.py index fec4b386..bee11c55 100644 --- a/src/obnb/data/ontology/base.py +++ b/src/obnb/data/ontology/base.py @@ -1,6 +1,6 @@ from obnb.data.base import BaseData from obnb.graph import OntologyGraph -from obnb.typing import List, Optional +from obnb.alltypes import List, Optional from obnb.util.download import stream_download diff --git a/src/obnb/dataset/base.py b/src/obnb/dataset/base.py index 39eddfee..824e3d38 100644 --- a/src/obnb/dataset/base.py +++ b/src/obnb/dataset/base.py @@ -8,7 +8,7 @@ from obnb.graph.base import BaseGraph from obnb.label.collection import LabelsetCollection from obnb.label.split.base import BaseSplit -from obnb.typing import ( +from obnb.alltypes import ( Any, Callable, Dict, diff --git a/src/obnb/dataset/dataset.py b/src/obnb/dataset/dataset.py index 660e8448..0ad171eb 100644 --- a/src/obnb/dataset/dataset.py +++ b/src/obnb/dataset/dataset.py @@ -3,7 +3,7 @@ import obnb.label.split from obnb.dataset.base import Dataset from obnb.label import filters -from obnb.typing import Any, Callable, Dict, List, LogLevel, Optional +from obnb.alltypes import Any, Callable, Dict, List, LogLevel, Optional from obnb.util.converter import GenePropertyConverter from obnb.util.misc import default from obnb.util.version import parse_data_version diff --git a/src/obnb/dataset/dataset_dgl.py b/src/obnb/dataset/dataset_dgl.py index 6e904812..96f6e89a 100644 --- a/src/obnb/dataset/dataset_dgl.py +++ b/src/obnb/dataset/dataset_dgl.py @@ -10,7 +10,7 @@ DGLDataset = object from obnb.dataset import OpenBiomedNetBench -from obnb.typing import Callable, LogLevel, Optional +from obnb.alltypes import Callable, LogLevel, Optional from obnb.util.logger import verbose from obnb.util.version import parse_data_version diff --git a/src/obnb/dataset/dataset_pyg.py b/src/obnb/dataset/dataset_pyg.py index fb3aee91..672ea088 100644 --- a/src/obnb/dataset/dataset_pyg.py +++ b/src/obnb/dataset/dataset_pyg.py @@ -8,7 +8,7 @@ InMemoryDataset = object from obnb.dataset import OpenBiomedNetBench -from obnb.typing import Callable, LogLevel, Optional +from obnb.alltypes import Callable, LogLevel, Optional from obnb.util.logger import verbose from obnb.util.version import parse_data_version diff --git a/src/obnb/ext/grape.py b/src/obnb/ext/grape.py index 7c277eb5..f12dd7f3 100644 --- a/src/obnb/ext/grape.py +++ b/src/obnb/ext/grape.py @@ -10,7 +10,7 @@ from obnb.feature import FeatureVec from obnb.graph.sparse import SparseGraph -from obnb.typing import Type, Union +from obnb.alltypes import Type, Union # Tested methods, see test/ext/test_grape.py VALIDATED_EMBEDDERS = [ diff --git a/src/obnb/ext/orbital_features.py b/src/obnb/ext/orbital_features.py index 743a6aa9..badaff7a 100644 --- a/src/obnb/ext/orbital_features.py +++ b/src/obnb/ext/orbital_features.py @@ -132,7 +132,7 @@ def setup_features(self): """Count orbital degrees.""" logger.info("Counting orbital roles.") self.features = { - node: {i: 0 for i in range(self.unique_motif_count)} + node: dict.fromkeys(range(self.unique_motif_count), 0) for node in self.graph.nodes() } for size, node_lists in self.edge_subsets.items(): diff --git a/src/obnb/ext/pecanpy.py b/src/obnb/ext/pecanpy.py index 41fa934d..27d41acf 100644 --- a/src/obnb/ext/pecanpy.py +++ b/src/obnb/ext/pecanpy.py @@ -5,7 +5,7 @@ from obnb.feature import FeatureVec from obnb.graph import DenseGraph, SparseGraph -from obnb.typing import Literal, Optional, Union +from obnb.alltypes import Literal, Optional, Union PECANPY_MODES = Literal[ "PreComp", diff --git a/src/obnb/ext/sknetwork.py b/src/obnb/ext/sknetwork.py index cac764c5..ca2f5da4 100644 --- a/src/obnb/ext/sknetwork.py +++ b/src/obnb/ext/sknetwork.py @@ -5,7 +5,7 @@ from obnb.feature import FeatureVec from obnb.graph import DenseGraph, SparseGraph -from obnb.typing import Literal, Union +from obnb.alltypes import Literal, Union SKNETWORK_EMBEDDINGS = Literal[ "Spectral", diff --git a/src/obnb/feature/base.py b/src/obnb/feature/base.py index 2deaf0f3..0691a250 100644 --- a/src/obnb/feature/base.py +++ b/src/obnb/feature/base.py @@ -4,7 +4,7 @@ import numpy as np -from obnb.typing import INT_TYPE, Iterable, List, LogLevel, Optional, Tuple, Union +from obnb.alltypes import INT_TYPE, Iterable, List, LogLevel, Optional, Tuple, Union from obnb.util import checkers from obnb.util.idhandler import IDmap from obnb.util.logger import get_logger diff --git a/src/obnb/feature/multifeat.py b/src/obnb/feature/multifeat.py index 58e40aae..e92200f8 100644 --- a/src/obnb/feature/multifeat.py +++ b/src/obnb/feature/multifeat.py @@ -4,7 +4,7 @@ import numpy as np from obnb.feature.base import BaseFeature -from obnb.typing import Iterable, List, LogLevel, Optional, Tuple, Union +from obnb.alltypes import Iterable, List, LogLevel, Optional, Tuple, Union from obnb.util.idhandler import IDmap diff --git a/src/obnb/feature/singlefeat.py b/src/obnb/feature/singlefeat.py index 42907dba..26c62149 100644 --- a/src/obnb/feature/singlefeat.py +++ b/src/obnb/feature/singlefeat.py @@ -2,7 +2,7 @@ import numpy as np from obnb.feature.base import BaseFeature -from obnb.typing import Iterable, LogLevel, Optional, Union +from obnb.alltypes import Iterable, LogLevel, Optional, Union class FeatureVec(BaseFeature): diff --git a/src/obnb/graph/base.py b/src/obnb/graph/base.py index 1c066ba6..5cec01dc 100644 --- a/src/obnb/graph/base.py +++ b/src/obnb/graph/base.py @@ -2,7 +2,7 @@ from copy import deepcopy from obnb.exception import IDExistsError -from obnb.typing import EdgeDir, Iterable, List, LogLevel, Optional, Tuple, Union +from obnb.alltypes import EdgeDir, Iterable, List, LogLevel, Optional, Tuple, Union from obnb.util import checkers, idhandler from obnb.util.checkers import checkLiteral from obnb.util.logger import get_logger diff --git a/src/obnb/graph/dense.py b/src/obnb/graph/dense.py index 1e98418e..399e5246 100644 --- a/src/obnb/graph/dense.py +++ b/src/obnb/graph/dense.py @@ -6,7 +6,7 @@ from obnb.feature import FeatureVec from obnb.graph.base import BaseGraph from obnb.graph.sparse import SparseGraph -from obnb.typing import EdgeDir, List, LogLevel, Optional, Union +from obnb.alltypes import EdgeDir, List, LogLevel, Optional, Union from obnb.util import checkers from obnb.util.idhandler import IDmap diff --git a/src/obnb/graph/ontology.py b/src/obnb/graph/ontology.py index eb07c6b8..e8cc4730 100644 --- a/src/obnb/graph/ontology.py +++ b/src/obnb/graph/ontology.py @@ -8,7 +8,7 @@ from obnb.exception import OboTermIncompleteError from obnb.graph.sparse import DirectedSparseGraph -from obnb.typing import ( +from obnb.alltypes import ( Dict, Iterable, Iterator, diff --git a/src/obnb/graph/sparse.py b/src/obnb/graph/sparse.py index 180a9d47..247e5bcf 100644 --- a/src/obnb/graph/sparse.py +++ b/src/obnb/graph/sparse.py @@ -7,7 +7,7 @@ from obnb.exception import EdgeNotExistError, IDNotExistError from obnb.graph.base import BaseGraph -from obnb.typing import ( +from obnb.alltypes import ( EdgeData, EdgeDir, Iterator, diff --git a/src/obnb/label/collection.py b/src/obnb/label/collection.py index d75ed1c1..387e3c63 100644 --- a/src/obnb/label/collection.py +++ b/src/obnb/label/collection.py @@ -7,7 +7,7 @@ from obnb.exception import IDExistsError from obnb.graph import OntologyGraph from obnb.label.filters.base import BaseFilter -from obnb.typing import Dict, Iterator, List, Optional, Set, Splitter, Tuple, Union +from obnb.alltypes import Dict, Iterator, List, Optional, Set, Splitter, Tuple, Union from obnb.util import checkers, idhandler diff --git a/src/obnb/label/filters/base.py b/src/obnb/label/filters/base.py index 9bc02282..4915100b 100644 --- a/src/obnb/label/filters/base.py +++ b/src/obnb/label/filters/base.py @@ -1,6 +1,6 @@ from tqdm import tqdm -from obnb.typing import Any, Dict, List, LogLevel +from obnb.alltypes import Any, Dict, List, LogLevel from obnb.util.logger import get_logger diff --git a/src/obnb/label/filters/existence_filter.py b/src/obnb/label/filters/existence_filter.py index 31c337bb..608e6aca 100644 --- a/src/obnb/label/filters/existence_filter.py +++ b/src/obnb/label/filters/existence_filter.py @@ -1,5 +1,5 @@ from obnb.label.filters.base import BaseFilter -from obnb.typing import List +from obnb.alltypes import List class BaseExistenceFilter(BaseFilter): diff --git a/src/obnb/label/filters/negative_generator.py b/src/obnb/label/filters/negative_generator.py index 5667f443..f88137d3 100644 --- a/src/obnb/label/filters/negative_generator.py +++ b/src/obnb/label/filters/negative_generator.py @@ -5,7 +5,7 @@ from tqdm import tqdm from obnb.label.filters.base import BaseFilter -from obnb.typing import List +from obnb.alltypes import List class NegativeGeneratorHypergeom(BaseFilter): diff --git a/src/obnb/label/filters/nonred.py b/src/obnb/label/filters/nonred.py index 4bbcb059..8fe2fc32 100644 --- a/src/obnb/label/filters/nonred.py +++ b/src/obnb/label/filters/nonred.py @@ -4,7 +4,7 @@ from obnb.graph import SparseGraph from obnb.label.collection import LabelsetCollection from obnb.label.filters.base import BaseFilter -from obnb.typing import List, Set, Tuple +from obnb.alltypes import List, Set, Tuple class LabelsetNonRedFilter(BaseFilter): diff --git a/src/obnb/label/filters/pairwise_filter.py b/src/obnb/label/filters/pairwise_filter.py index 2df7535c..780206bb 100644 --- a/src/obnb/label/filters/pairwise_filter.py +++ b/src/obnb/label/filters/pairwise_filter.py @@ -1,7 +1,7 @@ import numpy as np from obnb.label.filters.range_filter import BaseRangeFilter -from obnb.typing import Set +from obnb.alltypes import Set class BaseLabelsetPairwiseFilter(BaseRangeFilter): diff --git a/src/obnb/label/filters/range_filter.py b/src/obnb/label/filters/range_filter.py index dac802c0..7750d438 100644 --- a/src/obnb/label/filters/range_filter.py +++ b/src/obnb/label/filters/range_filter.py @@ -2,7 +2,7 @@ from obnb.label.collection import Splitter from obnb.label.filters.base import BaseFilter -from obnb.typing import List, Optional +from obnb.alltypes import List, Optional class BaseRangeFilter(BaseFilter): diff --git a/src/obnb/label/filters/value_filter.py b/src/obnb/label/filters/value_filter.py index ac2fa1a5..cf11b614 100644 --- a/src/obnb/label/filters/value_filter.py +++ b/src/obnb/label/filters/value_filter.py @@ -1,5 +1,5 @@ from obnb.label.filters.base import BaseFilter -from obnb.typing import List +from obnb.alltypes import List class BaseValueFilter(BaseFilter): diff --git a/src/obnb/label/split/base.py b/src/obnb/label/split/base.py index 6bb3259c..b6f8c309 100644 --- a/src/obnb/label/split/base.py +++ b/src/obnb/label/split/base.py @@ -2,7 +2,7 @@ import numpy as np -from obnb.typing import Any, Iterator, List, Mapping, Optional, Tuple, Union +from obnb.alltypes import Any, Iterator, List, Mapping, Optional, Tuple, Union from obnb.util.converter import BaseConverter diff --git a/src/obnb/label/split/holdout.py b/src/obnb/label/split/holdout.py index 01494ebc..847a3edc 100644 --- a/src/obnb/label/split/holdout.py +++ b/src/obnb/label/split/holdout.py @@ -1,7 +1,7 @@ import numpy as np from obnb.label.split.base import BaseRandomSplit, BaseSortedSplit -from obnb.typing import Tuple +from obnb.alltypes import Tuple from obnb.util.checkers import checkType diff --git a/src/obnb/label/split/partition.py b/src/obnb/label/split/partition.py index d942101f..7d5f06b7 100644 --- a/src/obnb/label/split/partition.py +++ b/src/obnb/label/split/partition.py @@ -3,7 +3,7 @@ import numpy as np from obnb.label.split.base import BaseRandomSplit, BaseSortedSplit -from obnb.typing import List, Tuple +from obnb.alltypes import List, Tuple from obnb.util.checkers import checkTypesInIterableErrEmpty diff --git a/src/obnb/metric/graphgym_metric.py b/src/obnb/metric/graphgym_metric.py index 1578ee5c..840b393b 100644 --- a/src/obnb/metric/graphgym_metric.py +++ b/src/obnb/metric/graphgym_metric.py @@ -5,7 +5,7 @@ from torch import Tensor from obnb.metric.standard import auroc, log2_auprc_prior, precision_at_topk -from obnb.typing import List, Metric +from obnb.alltypes import List, Metric __all__ = [ "graphgym_auroc", diff --git a/src/obnb/metric/standard.py b/src/obnb/metric/standard.py index 070344c2..2f9b4aab 100644 --- a/src/obnb/metric/standard.py +++ b/src/obnb/metric/standard.py @@ -8,7 +8,7 @@ import numpy as np import sklearn.metrics -from obnb.typing import Optional, Tensor, Union +from obnb.alltypes import Optional, Tensor, Union def cast_ndarray_type(x: Union[np.ndarray, Tensor]) -> np.ndarray: diff --git a/src/obnb/model_trainer/base.py b/src/obnb/model_trainer/base.py index e80a1f65..41f227f1 100644 --- a/src/obnb/model_trainer/base.py +++ b/src/obnb/model_trainer/base.py @@ -5,7 +5,7 @@ from tqdm.auto import tqdm import obnb.metric -from obnb.typing import Any, Callable, Dict, LogLevel, Optional +from obnb.alltypes import Any, Callable, Dict, LogLevel, Optional from obnb.util.logger import attach_file_handler, get_logger diff --git a/src/obnb/model_trainer/gnn.py b/src/obnb/model_trainer/gnn.py index 7a8b5486..25179802 100644 --- a/src/obnb/model_trainer/gnn.py +++ b/src/obnb/model_trainer/gnn.py @@ -4,7 +4,7 @@ import torch from obnb.model_trainer.base import BaseTrainer -from obnb.typing import Any, Callable, Dict, List, LogLevel, Optional, Tuple +from obnb.alltypes import Any, Callable, Dict, List, LogLevel, Optional, Tuple class GNNTrainer(BaseTrainer): diff --git a/src/obnb/model_trainer/graphgym.py b/src/obnb/model_trainer/graphgym.py index 447b36d0..58560ee6 100644 --- a/src/obnb/model_trainer/graphgym.py +++ b/src/obnb/model_trainer/graphgym.py @@ -19,7 +19,7 @@ from torch_geometric.graphgym.utils.device import auto_select_device from obnb.model_trainer.gnn import GNNTrainer -from obnb.typing import Any, Dict, List, Optional +from obnb.alltypes import Any, Dict, List, Optional def _patch_gg_makedirs_rm_exist(dir_): # patch for PyG<2.1.0 diff --git a/src/obnb/model_trainer/label_propagation.py b/src/obnb/model_trainer/label_propagation.py index fd90282e..c84f3f8e 100644 --- a/src/obnb/model_trainer/label_propagation.py +++ b/src/obnb/model_trainer/label_propagation.py @@ -1,7 +1,7 @@ import numpy as np from obnb.model_trainer.base import StandardTrainer -from obnb.typing import Callable, Dict, LogLevel, Optional +from obnb.alltypes import Callable, Dict, LogLevel, Optional class LabelPropagationTrainer(StandardTrainer): diff --git a/src/obnb/model_trainer/supervised_learning.py b/src/obnb/model_trainer/supervised_learning.py index d8486119..3dbc4898 100644 --- a/src/obnb/model_trainer/supervised_learning.py +++ b/src/obnb/model_trainer/supervised_learning.py @@ -1,7 +1,7 @@ import numpy as np from obnb.model_trainer.base import StandardTrainer -from obnb.typing import Callable, Dict, LogLevel, Optional +from obnb.alltypes import Callable, Dict, LogLevel, Optional class SupervisedLearningTrainer(StandardTrainer): diff --git a/src/obnb/registry.py b/src/obnb/registry.py index 8f84bef4..3b92af83 100644 --- a/src/obnb/registry.py +++ b/src/obnb/registry.py @@ -3,7 +3,7 @@ Helps interface with user defined modules for OBNB pipelines. """ -from obnb.typing import Any +from obnb.alltypes import Any from obnb.util.misc import DotDict REGISTRIES = DotDict() diff --git a/src/obnb/transform/base.py b/src/obnb/transform/base.py index 30be8d8f..5a684568 100644 --- a/src/obnb/transform/base.py +++ b/src/obnb/transform/base.py @@ -1,7 +1,7 @@ from abc import ABC, abstractmethod # from obnb.dataset.base import Dataset -from obnb.typing import LogLevel, Optional +from obnb.alltypes import LogLevel, Optional from obnb.util.logger import get_logger from obnb.util.misc import get_random_state diff --git a/src/obnb/transform/node_feature.py b/src/obnb/transform/node_feature.py index 6ddc4d02..ab9ded03 100644 --- a/src/obnb/transform/node_feature.py +++ b/src/obnb/transform/node_feature.py @@ -12,7 +12,7 @@ from obnb.feature import FeatureVec from obnb.registry import register_nodefeat from obnb.transform.base import BaseDatasetTransform -from obnb.typing import Optional +from obnb.alltypes import Optional from obnb.util.logger import display_pbar from obnb.util.misc import get_num_workers diff --git a/src/obnb/util/checkers.py b/src/obnb/util/checkers.py index 81fbf4b2..8e073d5a 100755 --- a/src/obnb/util/checkers.py +++ b/src/obnb/util/checkers.py @@ -10,7 +10,7 @@ import numpy as np -from obnb.typing import INT_TYPE, NUMERIC_TYPE, Iterable, List, Optional, Tuple +from obnb.alltypes import INT_TYPE, NUMERIC_TYPE, Iterable, List, Optional, Tuple __all__ = [ "checkConfig", diff --git a/src/obnb/util/converter.py b/src/obnb/util/converter.py index 27b88576..5ed3d7e0 100644 --- a/src/obnb/util/converter.py +++ b/src/obnb/util/converter.py @@ -8,7 +8,7 @@ import mygene import pandas as pd -from obnb.typing import Any, Dict, Iterator, List, LogLevel, Optional +from obnb.alltypes import Any, Dict, Iterator, List, LogLevel, Optional from obnb.util.checkers import checkType from obnb.util.logger import get_logger diff --git a/src/obnb/util/cx_explorer.py b/src/obnb/util/cx_explorer.py index f6f24a3b..10ace908 100644 --- a/src/obnb/util/cx_explorer.py +++ b/src/obnb/util/cx_explorer.py @@ -8,7 +8,7 @@ import ndex2 from requests import RequestException -from obnb.typing import Dict, List, Optional, Set +from obnb.alltypes import Dict, List, Optional, Set class CXExplorer: diff --git a/src/obnb/util/download.py b/src/obnb/util/download.py index a44792e4..b6b29d97 100644 --- a/src/obnb/util/download.py +++ b/src/obnb/util/download.py @@ -20,7 +20,7 @@ STREAM_BLOCK_SIZE, ) from obnb.exception import DataNotFoundError, ExceededMaxNumRetries -from obnb.typing import LogLevel, Optional, Tuple, ZipType +from obnb.alltypes import LogLevel, Optional, Tuple, ZipType from obnb.util.logger import display_pbar, get_logger native_logger = get_logger(None, log_level="INFO") diff --git a/src/obnb/util/idhandler.py b/src/obnb/util/idhandler.py index 9edff24d..db927dd1 100755 --- a/src/obnb/util/idhandler.py +++ b/src/obnb/util/idhandler.py @@ -5,7 +5,7 @@ import numpy as np from obnb.exception import IDExistsError, IDNotExistError -from obnb.typing import Dict, Iterable, List +from obnb.alltypes import Dict, Iterable, List from obnb.util import checkers __all__ = ["IDlst", "IDmap", "IDprop"] diff --git a/src/obnb/util/logger.py b/src/obnb/util/logger.py index ebc0dc7e..f48cf391 100644 --- a/src/obnb/util/logger.py +++ b/src/obnb/util/logger.py @@ -5,7 +5,7 @@ from contextlib import contextmanager from obnb.config.logger_config import LOGGER_CONFIG -from obnb.typing import List, LogLevel, Optional, Union +from obnb.alltypes import List, LogLevel, Optional, Union def verbose(level: Union[int, str], threshold="INFO") -> bool: diff --git a/src/obnb/util/misc.py b/src/obnb/util/misc.py index f03abc8c..ad3686a5 100644 --- a/src/obnb/util/misc.py +++ b/src/obnb/util/misc.py @@ -3,7 +3,7 @@ import numpy as np -from obnb.typing import Any, Optional +from obnb.alltypes import Any, Optional class DotDict(dict): diff --git a/src/obnb/util/parallel.py b/src/obnb/util/parallel.py index 6b8bd1d0..341802cd 100755 --- a/src/obnb/util/parallel.py +++ b/src/obnb/util/parallel.py @@ -2,7 +2,7 @@ from tqdm import tqdm -from obnb.typing import Any, Iterator, List, Tuple +from obnb.alltypes import Any, Iterator, List, Tuple from obnb.util import checkers mp.set_start_method("fork") diff --git a/src/obnb/util/registers.py b/src/obnb/util/registers.py index 9c3aaf81..7df392e0 100644 --- a/src/obnb/util/registers.py +++ b/src/obnb/util/registers.py @@ -1,6 +1,6 @@ import typing -from obnb.typing import Optional, Type +from obnb.alltypes import Optional, Type @typing.no_type_check # issue with Type diff --git a/src/obnb/util/resolver.py b/src/obnb/util/resolver.py index 9ef62d1c..fdeeb3c0 100644 --- a/src/obnb/util/resolver.py +++ b/src/obnb/util/resolver.py @@ -2,7 +2,7 @@ from pprint import pformat from obnb.registry import REGISTRIES -from obnb.typing import Any, Dict, Optional, Union +from obnb.alltypes import Any, Dict, Optional, Union def resolve_registry(name: str, scope: Optional[str] = None, verbose: bool = True): diff --git a/src/obnb/util/version.py b/src/obnb/util/version.py index 83d1ce15..13e31084 100644 --- a/src/obnb/util/version.py +++ b/src/obnb/util/version.py @@ -1,6 +1,6 @@ """Version utility module for obnb.""" from obnb import config -from obnb.typing import List +from obnb.alltypes import List def parse_data_version(version: str = "current") -> str: diff --git a/test/test_util/test_checkers.py b/test/test_util/test_checkers.py index 744fb681..4dea3d84 100644 --- a/test/test_util/test_checkers.py +++ b/test/test_util/test_checkers.py @@ -2,7 +2,7 @@ import numpy as np -from obnb.typing import FLOAT_TYPE, INT_TYPE, Iterable +from obnb.alltypes import FLOAT_TYPE, INT_TYPE, Iterable from obnb.util import checkers diff --git a/test/util/checkers/test_check_values.py b/test/util/checkers/test_check_values.py index b3b4e8be..c02d887b 100644 --- a/test/util/checkers/test_check_values.py +++ b/test/util/checkers/test_check_values.py @@ -1,6 +1,6 @@ import pytest -from obnb.typing import Literal +from obnb.alltypes import Literal from obnb.util.checkers import checkLiteral From c62c280ba6eb67b665417e4aa7a6ddc7a63ffe11 Mon Sep 17 00:00:00 2001 From: Faisal Alquaddoomi Date: Wed, 4 Dec 2024 10:55:09 -0700 Subject: [PATCH 2/4] Updated hooks, which hopefully will fix pre-commit.ci failure --- .pre-commit-config.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d505a3e7..42fcf43d 100644 --- a/.pre-commit-config.yaml +++ b/.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 @@ -25,12 +25,12 @@ 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"] @@ -43,7 +43,7 @@ repos: 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 From 71961e88d42f45742a8c4d8d55dc4b6f9ab5933a Mon Sep 17 00:00:00 2001 From: Faisal Alquaddoomi Date: Wed, 4 Dec 2024 11:11:17 -0700 Subject: [PATCH 3/4] Bumps docformatter to current HEAD hash to resolve hook language issue in v1.7.5 release --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 42fcf43d..e2bdc8f3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -36,7 +36,7 @@ repos: args: ["--safe"] - repo: https://github.com/PyCQA/docformatter - rev: v1.7.5 + rev: eb1df347edd128b30cd3368dddc3aa65edcfac38 # v1.7.5 hooks: - id: docformatter name: Format docstring From c892b3bed38cc93f945df7196f4a80d8f16e1f73 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 4 Dec 2024 18:11:33 +0000 Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- CODE_OF_CONDUCT.md | 2 +- example/utils.py | 2 +- script/release_data.py | 2 +- src/obnb/__init__.py | 1 + src/obnb/alltypes.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/annotated_ontology/base.py | 2 +- src/obnb/data/annotated_ontology/diseases.py | 2 +- src/obnb/data/annotated_ontology/disgenet.py | 2 +- src/obnb/data/annotated_ontology/go.py | 2 +- src/obnb/data/annotated_ontology/hpo.py | 2 +- src/obnb/data/annotation/__init__.py | 1 + src/obnb/data/annotation/base.py | 2 +- src/obnb/data/annotation/diseases.py | 2 +- src/obnb/data/annotation/disgenet.py | 2 +- src/obnb/data/annotation/gene_ontology.py | 2 +- .../data/annotation/human_phenotype_ontology.py | 2 +- src/obnb/data/experimental/__init__.py | 1 + src/obnb/data/experimental/alevinfry.py | 2 +- src/obnb/data/network/__init__.py | 1 + src/obnb/data/network/base.py | 2 +- src/obnb/data/network/biogrid.py | 2 +- src/obnb/data/network/bioplex.py | 2 +- src/obnb/data/network/comppi.py | 2 +- src/obnb/data/network/consensuspathdb.py | 2 +- src/obnb/data/network/funcoup.py | 2 +- src/obnb/data/network/hippie.py | 2 +- src/obnb/data/network/humanbase.py | 2 +- src/obnb/data/network/humannet.py | 2 +- src/obnb/data/network/humap.py | 2 +- src/obnb/data/network/huri.py | 2 +- src/obnb/data/network/omnipath.py | 2 +- src/obnb/data/network/pcnet.py | 2 +- src/obnb/data/network/proteomehd.py | 2 +- src/obnb/data/network/signor.py | 2 +- src/obnb/data/network/stringprot.py | 2 +- src/obnb/data/ontology/__init__.py | 1 + src/obnb/data/ontology/base.py | 2 +- src/obnb/dataset/__init__.py | 1 + src/obnb/dataset/base.py | 13 +++++++------ src/obnb/dataset/dataset.py | 3 ++- src/obnb/dataset/dataset_dgl.py | 3 ++- src/obnb/dataset/dataset_pyg.py | 3 ++- src/obnb/ext/attnwalk.py | 1 + src/obnb/ext/grape.py | 2 +- src/obnb/ext/orbital_features.py | 1 + src/obnb/ext/pecanpy.py | 2 +- src/obnb/ext/sknetwork.py | 2 +- src/obnb/feature/__init__.py | 1 + src/obnb/feature/multifeat.py | 3 ++- src/obnb/feature/singlefeat.py | 3 ++- src/obnb/graph/__init__.py | 1 + src/obnb/graph/base.py | 2 +- src/obnb/graph/dense.py | 2 +- src/obnb/graph/ontology.py | 4 ++-- src/obnb/graph/sparse.py | 4 ++-- src/obnb/label/__init__.py | 1 + src/obnb/label/collection.py | 2 +- src/obnb/label/filters/__init__.py | 1 + src/obnb/label/filters/existence_filter.py | 2 +- src/obnb/label/filters/negative_generator.py | 2 +- src/obnb/label/filters/nonred.py | 2 +- src/obnb/label/filters/pairwise_filter.py | 2 +- src/obnb/label/filters/range_filter.py | 6 +++--- src/obnb/label/filters/value_filter.py | 2 +- src/obnb/label/split/__init__.py | 1 + src/obnb/label/split/holdout.py | 2 +- src/obnb/label/split/partition.py | 2 +- src/obnb/metric/__init__.py | 1 + src/obnb/metric/graphgym_metric.py | 3 ++- src/obnb/metric/standard.py | 1 + src/obnb/model_trainer/__init__.py | 1 + src/obnb/model_trainer/gnn.py | 2 +- src/obnb/model_trainer/graphgym.py | 2 +- src/obnb/model_trainer/label_propagation.py | 2 +- src/obnb/model_trainer/supervised_learning.py | 2 +- src/obnb/registry.py | 1 + src/obnb/transform/base.py | 3 +-- src/obnb/transform/node_feature.py | 6 +++--- src/obnb/util/checkers.py | 1 + src/obnb/util/cx_explorer.py | 1 + src/obnb/util/download.py | 2 +- src/obnb/util/idhandler.py | 2 +- src/obnb/util/logger.py | 3 ++- src/obnb/util/path.py | 1 + src/obnb/util/resolver.py | 2 +- src/obnb/util/version.py | 1 + 89 files changed, 108 insertions(+), 76 deletions(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 225b23bb..3985e44a 100644 --- a/CODE_OF_CONDUCT.md +++ b/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 diff --git a/example/utils.py b/example/utils.py index 4a12945b..99c7e3c9 100644 --- a/example/utils.py +++ b/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.alltypes import LogLevel from obnb.util.converter import GenePropertyConverter diff --git a/script/release_data.py b/script/release_data.py index bdd2433a..8231d15e 100644 --- a/script/release_data.py +++ b/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.alltypes import Dict, List, Tuple from obnb.util.converter import GenePropertyConverter HOMEDIR = Path(__file__).resolve().parent 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/alltypes.py b/src/obnb/alltypes.py index 432a8a3f..bf81068b 100644 --- a/src/obnb/alltypes.py +++ b/src/obnb/alltypes.py @@ -1,4 +1,5 @@ """Collection of types used in obnb.""" + from typing import ( Any, Callable, diff --git a/src/obnb/config/__init__.py b/src/obnb/config/__init__.py index 4081f823..9e7e35ad 100644 --- a/src/obnb/config/__init__.py +++ b/src/obnb/config/__init__.py @@ -1,4 +1,5 @@ """Configurations used by obnb.""" + from obnb.alltypes 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/annotated_ontology/base.py b/src/obnb/data/annotated_ontology/base.py index cd0d25be..78cd3907 100644 --- a/src/obnb/data/annotated_ontology/base.py +++ b/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.alltypes import Any, Dict, List, Optional, Type from obnb.util.logger import display_pbar diff --git a/src/obnb/data/annotated_ontology/diseases.py b/src/obnb/data/annotated_ontology/diseases.py index c0f8dd6d..1d0617b7 100644 --- a/src/obnb/data/annotated_ontology/diseases.py +++ b/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.alltypes import Mapping, Optional, Union from obnb.util.registers import overload_class diff --git a/src/obnb/data/annotated_ontology/disgenet.py b/src/obnb/data/annotated_ontology/disgenet.py index 0d765a0c..92354ca5 100644 --- a/src/obnb/data/annotated_ontology/disgenet.py +++ b/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.alltypes import List, Mapping, Optional, Union from obnb.util.registers import overload_class diff --git a/src/obnb/data/annotated_ontology/go.py b/src/obnb/data/annotated_ontology/go.py index e621d0f6..90492e4c 100644 --- a/src/obnb/data/annotated_ontology/go.py +++ b/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.alltypes import List, Mapping, Optional, Union from obnb.util.registers import overload_class diff --git a/src/obnb/data/annotated_ontology/hpo.py b/src/obnb/data/annotated_ontology/hpo.py index fb027d66..80070783 100644 --- a/src/obnb/data/annotated_ontology/hpo.py +++ b/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.alltypes import List, Mapping, Optional, Union class HPO(BaseAnnotatedOntologyData): 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/annotation/base.py b/src/obnb/data/annotation/base.py index 39ef1202..9dbb80a5 100644 --- a/src/obnb/data/annotation/base.py +++ b/src/obnb/data/annotation/base.py @@ -1,5 +1,5 @@ -from obnb.data.base import BaseData from obnb.alltypes import List, Optional, ZipType +from obnb.data.base import BaseData from obnb.util.download import download_unzip diff --git a/src/obnb/data/annotation/diseases.py b/src/obnb/data/annotation/diseases.py index a626f331..d51c3625 100644 --- a/src/obnb/data/annotation/diseases.py +++ b/src/obnb/data/annotation/diseases.py @@ -2,8 +2,8 @@ import pandas as pd -from obnb.data.annotation.base import BaseAnnotationData from obnb.alltypes import List, Optional +from obnb.data.annotation.base import BaseAnnotationData class DISEASESAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/annotation/disgenet.py b/src/obnb/data/annotation/disgenet.py index e7e74945..3f6ebddc 100644 --- a/src/obnb/data/annotation/disgenet.py +++ b/src/obnb/data/annotation/disgenet.py @@ -2,8 +2,8 @@ import pandas as pd -from obnb.data.annotation.base import BaseAnnotationData from obnb.alltypes import List, Optional +from obnb.data.annotation.base import BaseAnnotationData class DisGeNETAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/annotation/gene_ontology.py b/src/obnb/data/annotation/gene_ontology.py index a98f3f15..91f01969 100644 --- a/src/obnb/data/annotation/gene_ontology.py +++ b/src/obnb/data/annotation/gene_ontology.py @@ -2,8 +2,8 @@ import pandas as pd -from obnb.data.annotation.base import BaseAnnotationData from obnb.alltypes import List, Optional +from obnb.data.annotation.base import BaseAnnotationData class GeneOntologyAnnotation(BaseAnnotationData): diff --git a/src/obnb/data/annotation/human_phenotype_ontology.py b/src/obnb/data/annotation/human_phenotype_ontology.py index 5360b7be..bc1a93c4 100644 --- a/src/obnb/data/annotation/human_phenotype_ontology.py +++ b/src/obnb/data/annotation/human_phenotype_ontology.py @@ -2,8 +2,8 @@ import pandas as pd -from obnb.data.annotation.base import BaseAnnotationData from obnb.alltypes import List, Optional +from obnb.data.annotation.base import BaseAnnotationData class HumanPhenotypeOntologyAnnotation(BaseAnnotationData): 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/experimental/alevinfry.py b/src/obnb/data/experimental/alevinfry.py index f5f41a0e..0a74d92a 100644 --- a/src/obnb/data/experimental/alevinfry.py +++ b/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.alltypes import Dict, List, Optional class AlevinFry(BaseData, FeatureVec): diff --git a/src/obnb/data/network/__init__.py b/src/obnb/data/network/__init__.py index fa842e22..c02c24ac 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/network/base.py b/src/obnb/data/network/base.py index d2f02af4..af9ec233 100644 --- a/src/obnb/data/network/base.py +++ b/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.alltypes import Any, Dict, List, Mapping, Optional, Union from obnb.util.download import download_unzip from obnb.util.logger import display_pbar diff --git a/src/obnb/data/network/biogrid.py b/src/obnb/data/network/biogrid.py index 3d8536b8..e5f028b0 100644 --- a/src/obnb/data/network/biogrid.py +++ b/src/obnb/data/network/biogrid.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class BioGRID(BaseNDExData): diff --git a/src/obnb/data/network/bioplex.py b/src/obnb/data/network/bioplex.py index 9b796e46..14d51e3c 100644 --- a/src/obnb/data/network/bioplex.py +++ b/src/obnb/data/network/bioplex.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class BioPlex(BaseNDExData): diff --git a/src/obnb/data/network/comppi.py b/src/obnb/data/network/comppi.py index ef5943b7..24a353c0 100644 --- a/src/obnb/data/network/comppi.py +++ b/src/obnb/data/network/comppi.py @@ -3,8 +3,8 @@ import pandas as pd import requests -from obnb.data.network.base import BaseURLSparseGraphData from obnb.alltypes import Any, Dict, List, Mapping, Optional, Union +from obnb.data.network.base import BaseURLSparseGraphData class ComPPI(BaseURLSparseGraphData): diff --git a/src/obnb/data/network/consensuspathdb.py b/src/obnb/data/network/consensuspathdb.py index f658ae5d..ac7ec5a0 100644 --- a/src/obnb/data/network/consensuspathdb.py +++ b/src/obnb/data/network/consensuspathdb.py @@ -4,8 +4,8 @@ import numpy as np import pandas as pd -from obnb.data.network.base import BaseURLSparseGraphData from obnb.alltypes import List, Literal, Mapping, Optional, Union +from obnb.data.network.base import BaseURLSparseGraphData from obnb.util.download import download_unzip diff --git a/src/obnb/data/network/funcoup.py b/src/obnb/data/network/funcoup.py index c7aaa82e..0ca9b619 100644 --- a/src/obnb/data/network/funcoup.py +++ b/src/obnb/data/network/funcoup.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class FunCoup(BaseNDExData): diff --git a/src/obnb/data/network/hippie.py b/src/obnb/data/network/hippie.py index 696b4851..43a06cdf 100644 --- a/src/obnb/data/network/hippie.py +++ b/src/obnb/data/network/hippie.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class HIPPIE(BaseNDExData): diff --git a/src/obnb/data/network/humanbase.py b/src/obnb/data/network/humanbase.py index 8a0d6a9c..6069f6c9 100644 --- a/src/obnb/data/network/humanbase.py +++ b/src/obnb/data/network/humanbase.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseURLSparseGraphData from obnb.alltypes import Converter +from obnb.data.network.base import BaseURLSparseGraphData class HumanBaseTopGlobal(BaseURLSparseGraphData): diff --git a/src/obnb/data/network/humannet.py b/src/obnb/data/network/humannet.py index 020aa6bb..a3ceabea 100644 --- a/src/obnb/data/network/humannet.py +++ b/src/obnb/data/network/humannet.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseURLSparseGraphData from obnb.alltypes import Converter, List +from obnb.data.network.base import BaseURLSparseGraphData from obnb.util.registers import overload_class diff --git a/src/obnb/data/network/humap.py b/src/obnb/data/network/humap.py index 44671bf1..1c57e56c 100644 --- a/src/obnb/data/network/humap.py +++ b/src/obnb/data/network/humap.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseURLSparseGraphData from obnb.alltypes import Converter +from obnb.data.network.base import BaseURLSparseGraphData class HuMAP(BaseURLSparseGraphData): diff --git a/src/obnb/data/network/huri.py b/src/obnb/data/network/huri.py index 5feee3df..af87586c 100644 --- a/src/obnb/data/network/huri.py +++ b/src/obnb/data/network/huri.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class HuRI(BaseNDExData): diff --git a/src/obnb/data/network/omnipath.py b/src/obnb/data/network/omnipath.py index d20d34ff..5ac528f1 100644 --- a/src/obnb/data/network/omnipath.py +++ b/src/obnb/data/network/omnipath.py @@ -3,8 +3,8 @@ import pandas as pd import requests -from obnb.data.network.base import BaseURLSparseGraphData from obnb.alltypes import List, Mapping, Optional, Union +from obnb.data.network.base import BaseURLSparseGraphData from obnb.util.download import stream_download diff --git a/src/obnb/data/network/pcnet.py b/src/obnb/data/network/pcnet.py index cc5cbf75..2e1b3479 100644 --- a/src/obnb/data/network/pcnet.py +++ b/src/obnb/data/network/pcnet.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class PCNet(BaseNDExData): diff --git a/src/obnb/data/network/proteomehd.py b/src/obnb/data/network/proteomehd.py index acc7740d..837736f6 100644 --- a/src/obnb/data/network/proteomehd.py +++ b/src/obnb/data/network/proteomehd.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class ProteomeHD(BaseNDExData): diff --git a/src/obnb/data/network/signor.py b/src/obnb/data/network/signor.py index acdc72c8..0b916a9e 100644 --- a/src/obnb/data/network/signor.py +++ b/src/obnb/data/network/signor.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class SIGNOR(BaseNDExData): diff --git a/src/obnb/data/network/stringprot.py b/src/obnb/data/network/stringprot.py index f3989a4e..682fc2e9 100644 --- a/src/obnb/data/network/stringprot.py +++ b/src/obnb/data/network/stringprot.py @@ -1,5 +1,5 @@ -from obnb.data.network.base import BaseNDExData from obnb.alltypes import Converter +from obnb.data.network.base import BaseNDExData class STRING(BaseNDExData): 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/data/ontology/base.py b/src/obnb/data/ontology/base.py index bee11c55..aa32550a 100644 --- a/src/obnb/data/ontology/base.py +++ b/src/obnb/data/ontology/base.py @@ -1,6 +1,6 @@ +from obnb.alltypes import List, Optional from obnb.data.base import BaseData from obnb.graph import OntologyGraph -from obnb.alltypes import List, Optional from obnb.util.download import stream_download 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 824e3d38..bc3da79c 100644 --- a/src/obnb/dataset/base.py +++ b/src/obnb/dataset/base.py @@ -1,13 +1,8 @@ """Dataset object.""" + import numpy as np from sklearn.preprocessing import KBinsDiscretizer -from obnb.feature import FeatureVec, MultiFeatureVec -from obnb.feature.base import BaseFeature -from obnb.graph import DenseGraph, SparseGraph -from obnb.graph.base import BaseGraph -from obnb.label.collection import LabelsetCollection -from obnb.label.split.base import BaseSplit from obnb.alltypes import ( Any, Callable, @@ -20,6 +15,12 @@ Tuple, Union, ) +from obnb.feature import FeatureVec, MultiFeatureVec +from obnb.feature.base import BaseFeature +from obnb.graph import DenseGraph, SparseGraph +from obnb.graph.base import BaseGraph +from obnb.label.collection import LabelsetCollection +from obnb.label.split.base import BaseSplit from obnb.util.checkers import checkLiteral, checkNumpyArrayShape, checkType from obnb.util.idhandler import IDmap from obnb.util.resolver import resolve_transform diff --git a/src/obnb/dataset/dataset.py b/src/obnb/dataset/dataset.py index 0ad171eb..26f6d66e 100644 --- a/src/obnb/dataset/dataset.py +++ b/src/obnb/dataset/dataset.py @@ -1,9 +1,10 @@ """Helper functions to construct processed datasets.""" + import obnb.data import obnb.label.split +from obnb.alltypes import Any, Callable, Dict, List, LogLevel, Optional from obnb.dataset.base import Dataset from obnb.label import filters -from obnb.alltypes import Any, Callable, Dict, List, LogLevel, Optional from obnb.util.converter import GenePropertyConverter from obnb.util.misc import default from obnb.util.version import parse_data_version diff --git a/src/obnb/dataset/dataset_dgl.py b/src/obnb/dataset/dataset_dgl.py index 96f6e89a..8f57e755 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: @@ -9,8 +10,8 @@ except (ModuleNotFoundError, OSError): DGLDataset = object -from obnb.dataset import OpenBiomedNetBench from obnb.alltypes import Callable, LogLevel, Optional +from obnb.dataset import OpenBiomedNetBench from obnb.util.logger import verbose from obnb.util.version import parse_data_version diff --git a/src/obnb/dataset/dataset_pyg.py b/src/obnb/dataset/dataset_pyg.py index 672ea088..9ff4ddd1 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: @@ -7,8 +8,8 @@ except (ModuleNotFoundError, OSError): InMemoryDataset = object -from obnb.dataset import OpenBiomedNetBench from obnb.alltypes import Callable, LogLevel, Optional +from obnb.dataset import OpenBiomedNetBench from obnb.util.logger import verbose from obnb.util.version import parse_data_version 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/grape.py b/src/obnb/ext/grape.py index f12dd7f3..1521c9b1 100644 --- a/src/obnb/ext/grape.py +++ b/src/obnb/ext/grape.py @@ -8,9 +8,9 @@ ) from ensmallen import Graph, GraphBuilder +from obnb.alltypes import Type, Union from obnb.feature import FeatureVec from obnb.graph.sparse import SparseGraph -from obnb.alltypes import Type, Union # Tested methods, see test/ext/test_grape.py VALIDATED_EMBEDDERS = [ diff --git a/src/obnb/ext/orbital_features.py b/src/obnb/ext/orbital_features.py index badaff7a..7ae5ca83 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/ext/pecanpy.py b/src/obnb/ext/pecanpy.py index 27d41acf..f43bbbec 100644 --- a/src/obnb/ext/pecanpy.py +++ b/src/obnb/ext/pecanpy.py @@ -3,9 +3,9 @@ import numpy as np from pecanpy import pecanpy +from obnb.alltypes import Literal, Optional, Union from obnb.feature import FeatureVec from obnb.graph import DenseGraph, SparseGraph -from obnb.alltypes import Literal, Optional, Union PECANPY_MODES = Literal[ "PreComp", diff --git a/src/obnb/ext/sknetwork.py b/src/obnb/ext/sknetwork.py index ca2f5da4..7a68eb7f 100644 --- a/src/obnb/ext/sknetwork.py +++ b/src/obnb/ext/sknetwork.py @@ -3,9 +3,9 @@ import numpy as np import sknetwork.embedding +from obnb.alltypes import Literal, Union from obnb.feature import FeatureVec from obnb.graph import DenseGraph, SparseGraph -from obnb.alltypes import Literal, Union SKNETWORK_EMBEDDINGS = Literal[ "Spectral", 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 e92200f8..ef904140 100644 --- a/src/obnb/feature/multifeat.py +++ b/src/obnb/feature/multifeat.py @@ -1,10 +1,11 @@ """Multi modality feature objects.""" + from itertools import chain import numpy as np -from obnb.feature.base import BaseFeature from obnb.alltypes import Iterable, List, LogLevel, Optional, Tuple, Union +from obnb.feature.base import BaseFeature from obnb.util.idhandler import IDmap diff --git a/src/obnb/feature/singlefeat.py b/src/obnb/feature/singlefeat.py index 26c62149..04828183 100644 --- a/src/obnb/feature/singlefeat.py +++ b/src/obnb/feature/singlefeat.py @@ -1,8 +1,9 @@ """Single modality feature objects.""" + import numpy as np -from obnb.feature.base import BaseFeature from obnb.alltypes import Iterable, LogLevel, Optional, Union +from obnb.feature.base import BaseFeature class FeatureVec(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/graph/base.py b/src/obnb/graph/base.py index 5cec01dc..1e890c88 100644 --- a/src/obnb/graph/base.py +++ b/src/obnb/graph/base.py @@ -1,8 +1,8 @@ import logging from copy import deepcopy -from obnb.exception import IDExistsError from obnb.alltypes import EdgeDir, Iterable, List, LogLevel, Optional, Tuple, Union +from obnb.exception import IDExistsError from obnb.util import checkers, idhandler from obnb.util.checkers import checkLiteral from obnb.util.logger import get_logger diff --git a/src/obnb/graph/dense.py b/src/obnb/graph/dense.py index 399e5246..94f2a74b 100644 --- a/src/obnb/graph/dense.py +++ b/src/obnb/graph/dense.py @@ -2,11 +2,11 @@ import numpy as np +from obnb.alltypes import EdgeDir, List, LogLevel, Optional, Union from obnb.exception import IDNotExistError from obnb.feature import FeatureVec from obnb.graph.base import BaseGraph from obnb.graph.sparse import SparseGraph -from obnb.alltypes import EdgeDir, List, LogLevel, Optional, Union from obnb.util import checkers from obnb.util.idhandler import IDmap diff --git a/src/obnb/graph/ontology.py b/src/obnb/graph/ontology.py index e8cc4730..ee00c638 100644 --- a/src/obnb/graph/ontology.py +++ b/src/obnb/graph/ontology.py @@ -6,8 +6,6 @@ from tqdm import trange -from obnb.exception import OboTermIncompleteError -from obnb.graph.sparse import DirectedSparseGraph from obnb.alltypes import ( Dict, Iterable, @@ -20,6 +18,8 @@ TextIO, Union, ) +from obnb.exception import OboTermIncompleteError +from obnb.graph.sparse import DirectedSparseGraph from obnb.util import idhandler diff --git a/src/obnb/graph/sparse.py b/src/obnb/graph/sparse.py index 247e5bcf..bef718b3 100644 --- a/src/obnb/graph/sparse.py +++ b/src/obnb/graph/sparse.py @@ -5,8 +5,6 @@ import numpy as np from tqdm import trange -from obnb.exception import EdgeNotExistError, IDNotExistError -from obnb.graph.base import BaseGraph from obnb.alltypes import ( EdgeData, EdgeDir, @@ -18,6 +16,8 @@ Tuple, Union, ) +from obnb.exception import EdgeNotExistError, IDNotExistError +from obnb.graph.base import BaseGraph from obnb.util import checkers from obnb.util.cx_explorer import CXExplorer from obnb.util.idhandler import IDmap 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/collection.py b/src/obnb/label/collection.py index 387e3c63..28bf937c 100644 --- a/src/obnb/label/collection.py +++ b/src/obnb/label/collection.py @@ -4,10 +4,10 @@ import numpy as np import pandas as pd +from obnb.alltypes import Dict, Iterator, List, Optional, Set, Splitter, Tuple, Union from obnb.exception import IDExistsError from obnb.graph import OntologyGraph from obnb.label.filters.base import BaseFilter -from obnb.alltypes import Dict, Iterator, List, Optional, Set, Splitter, Tuple, Union from obnb.util import checkers, idhandler 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/filters/existence_filter.py b/src/obnb/label/filters/existence_filter.py index 608e6aca..cd40810e 100644 --- a/src/obnb/label/filters/existence_filter.py +++ b/src/obnb/label/filters/existence_filter.py @@ -1,5 +1,5 @@ -from obnb.label.filters.base import BaseFilter from obnb.alltypes import List +from obnb.label.filters.base import BaseFilter class BaseExistenceFilter(BaseFilter): diff --git a/src/obnb/label/filters/negative_generator.py b/src/obnb/label/filters/negative_generator.py index f88137d3..4166246d 100644 --- a/src/obnb/label/filters/negative_generator.py +++ b/src/obnb/label/filters/negative_generator.py @@ -4,8 +4,8 @@ from scipy.stats import hypergeom from tqdm import tqdm -from obnb.label.filters.base import BaseFilter from obnb.alltypes import List +from obnb.label.filters.base import BaseFilter class NegativeGeneratorHypergeom(BaseFilter): diff --git a/src/obnb/label/filters/nonred.py b/src/obnb/label/filters/nonred.py index 8fe2fc32..354affff 100644 --- a/src/obnb/label/filters/nonred.py +++ b/src/obnb/label/filters/nonred.py @@ -1,10 +1,10 @@ from functools import partial from itertools import combinations +from obnb.alltypes import List, Set, Tuple from obnb.graph import SparseGraph from obnb.label.collection import LabelsetCollection from obnb.label.filters.base import BaseFilter -from obnb.alltypes import List, Set, Tuple class LabelsetNonRedFilter(BaseFilter): diff --git a/src/obnb/label/filters/pairwise_filter.py b/src/obnb/label/filters/pairwise_filter.py index 780206bb..e9c76b0e 100644 --- a/src/obnb/label/filters/pairwise_filter.py +++ b/src/obnb/label/filters/pairwise_filter.py @@ -1,7 +1,7 @@ import numpy as np -from obnb.label.filters.range_filter import BaseRangeFilter from obnb.alltypes import Set +from obnb.label.filters.range_filter import BaseRangeFilter class BaseLabelsetPairwiseFilter(BaseRangeFilter): diff --git a/src/obnb/label/filters/range_filter.py b/src/obnb/label/filters/range_filter.py index 7750d438..3169d3d0 100644 --- a/src/obnb/label/filters/range_filter.py +++ b/src/obnb/label/filters/range_filter.py @@ -1,8 +1,8 @@ import numpy as np +from obnb.alltypes import List, Optional from obnb.label.collection import Splitter from obnb.label.filters.base import BaseFilter -from obnb.alltypes import List, Optional class BaseRangeFilter(BaseFilter): @@ -164,7 +164,7 @@ 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)] - self.logger.debug(f"{label_id = } {neg_idx = }") + self.logger.debug(f"{label_id =} {neg_idx =}") # TODO: make label_ids to index mapping? y = y_all[:, lsc.label_ids.index(label_id)] min_num_pos = min_num_neg = np.inf @@ -175,7 +175,7 @@ def val_getter(label_id): min_num_pos = min(min_num_pos, num_pos) if self.count_negatives: num_neg = np.intersect1d(neg_idx, masked_idx).size - self.logger.debug(f"{num_neg = }, {masked_idx = }") + self.logger.debug(f"{num_neg =}, {masked_idx =}") min_num_neg = min(min_num_neg, num_neg) self.logger.info(f"{label_id}, {min_num_pos=}, {min_num_neg=}") return min(min_num_pos, min_num_neg) diff --git a/src/obnb/label/filters/value_filter.py b/src/obnb/label/filters/value_filter.py index cf11b614..f4fca46b 100644 --- a/src/obnb/label/filters/value_filter.py +++ b/src/obnb/label/filters/value_filter.py @@ -1,5 +1,5 @@ -from obnb.label.filters.base import BaseFilter from obnb.alltypes import List +from obnb.label.filters.base import BaseFilter class BaseValueFilter(BaseFilter): 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/label/split/holdout.py b/src/obnb/label/split/holdout.py index 847a3edc..5b4ef9ff 100644 --- a/src/obnb/label/split/holdout.py +++ b/src/obnb/label/split/holdout.py @@ -1,7 +1,7 @@ import numpy as np -from obnb.label.split.base import BaseRandomSplit, BaseSortedSplit from obnb.alltypes import Tuple +from obnb.label.split.base import BaseRandomSplit, BaseSortedSplit from obnb.util.checkers import checkType diff --git a/src/obnb/label/split/partition.py b/src/obnb/label/split/partition.py index 7d5f06b7..e4659000 100644 --- a/src/obnb/label/split/partition.py +++ b/src/obnb/label/split/partition.py @@ -2,8 +2,8 @@ import numpy as np -from obnb.label.split.base import BaseRandomSplit, BaseSortedSplit from obnb.alltypes import List, Tuple +from obnb.label.split.base import BaseRandomSplit, BaseSortedSplit from obnb.util.checkers import checkTypesInIterableErrEmpty 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 840b393b..a19d622b 100644 --- a/src/obnb/metric/graphgym_metric.py +++ b/src/obnb/metric/graphgym_metric.py @@ -1,11 +1,12 @@ """Custom metrics compatible with GraphGym logger.""" + from functools import wraps import torch from torch import Tensor -from obnb.metric.standard import auroc, log2_auprc_prior, precision_at_topk from obnb.alltypes import List, Metric +from obnb.metric.standard import auroc, log2_auprc_prior, precision_at_topk __all__ = [ "graphgym_auroc", diff --git a/src/obnb/metric/standard.py b/src/obnb/metric/standard.py index 2f9b4aab..f6ff712c 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/model_trainer/gnn.py b/src/obnb/model_trainer/gnn.py index 25179802..66eb74d0 100644 --- a/src/obnb/model_trainer/gnn.py +++ b/src/obnb/model_trainer/gnn.py @@ -3,8 +3,8 @@ import numpy as np import torch -from obnb.model_trainer.base import BaseTrainer from obnb.alltypes import Any, Callable, Dict, List, LogLevel, Optional, Tuple +from obnb.model_trainer.base import BaseTrainer class GNNTrainer(BaseTrainer): diff --git a/src/obnb/model_trainer/graphgym.py b/src/obnb/model_trainer/graphgym.py index 58560ee6..9fd8484c 100644 --- a/src/obnb/model_trainer/graphgym.py +++ b/src/obnb/model_trainer/graphgym.py @@ -18,8 +18,8 @@ from torch_geometric.graphgym.utils.comp_budget import params_count from torch_geometric.graphgym.utils.device import auto_select_device -from obnb.model_trainer.gnn import GNNTrainer from obnb.alltypes import Any, Dict, List, Optional +from obnb.model_trainer.gnn import GNNTrainer def _patch_gg_makedirs_rm_exist(dir_): # patch for PyG<2.1.0 diff --git a/src/obnb/model_trainer/label_propagation.py b/src/obnb/model_trainer/label_propagation.py index c84f3f8e..e00e4b39 100644 --- a/src/obnb/model_trainer/label_propagation.py +++ b/src/obnb/model_trainer/label_propagation.py @@ -1,7 +1,7 @@ import numpy as np -from obnb.model_trainer.base import StandardTrainer from obnb.alltypes import Callable, Dict, LogLevel, Optional +from obnb.model_trainer.base import StandardTrainer class LabelPropagationTrainer(StandardTrainer): diff --git a/src/obnb/model_trainer/supervised_learning.py b/src/obnb/model_trainer/supervised_learning.py index 3dbc4898..0e99c260 100644 --- a/src/obnb/model_trainer/supervised_learning.py +++ b/src/obnb/model_trainer/supervised_learning.py @@ -1,7 +1,7 @@ import numpy as np -from obnb.model_trainer.base import StandardTrainer from obnb.alltypes import Callable, Dict, LogLevel, Optional +from obnb.model_trainer.base import StandardTrainer class SupervisedLearningTrainer(StandardTrainer): diff --git a/src/obnb/registry.py b/src/obnb/registry.py index 3b92af83..1c980169 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.alltypes import Any from obnb.util.misc import DotDict diff --git a/src/obnb/transform/base.py b/src/obnb/transform/base.py index 5a684568..12919df2 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 ab9ded03..2909e9b3 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 @@ -9,10 +10,10 @@ from sklearn.random_projection import GaussianRandomProjection, SparseRandomProjection import obnb +from obnb.alltypes import Optional from obnb.feature import FeatureVec from obnb.registry import register_nodefeat from obnb.transform.base import BaseDatasetTransform -from obnb.alltypes import Optional from obnb.util.logger import display_pbar from obnb.util.misc import get_num_workers @@ -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/util/checkers.py b/src/obnb/util/checkers.py index 8e073d5a..7d4dad55 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 10ace908..ecf20f8c 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/download.py b/src/obnb/util/download.py index b6b29d97..de36edd1 100644 --- a/src/obnb/util/download.py +++ b/src/obnb/util/download.py @@ -12,6 +12,7 @@ import requests from tqdm import tqdm +from obnb.alltypes import LogLevel, Optional, Tuple, ZipType from obnb.config import ( DEFAULT_RETRY_DELAY, MAX_DOWNLOAD_RETRIES, @@ -20,7 +21,6 @@ STREAM_BLOCK_SIZE, ) from obnb.exception import DataNotFoundError, ExceededMaxNumRetries -from obnb.alltypes import LogLevel, Optional, Tuple, ZipType from obnb.util.logger import display_pbar, get_logger native_logger = get_logger(None, log_level="INFO") diff --git a/src/obnb/util/idhandler.py b/src/obnb/util/idhandler.py index db927dd1..6fd81696 100755 --- a/src/obnb/util/idhandler.py +++ b/src/obnb/util/idhandler.py @@ -4,8 +4,8 @@ import numpy as np -from obnb.exception import IDExistsError, IDNotExistError from obnb.alltypes import Dict, Iterable, List +from obnb.exception import IDExistsError, IDNotExistError from obnb.util import checkers __all__ = ["IDlst", "IDmap", "IDprop"] diff --git a/src/obnb/util/logger.py b/src/obnb/util/logger.py index f48cf391..7d73d8c2 100644 --- a/src/obnb/util/logger.py +++ b/src/obnb/util/logger.py @@ -1,11 +1,12 @@ """Logger utils.""" + import logging import logging.config import os from contextlib import contextmanager -from obnb.config.logger_config import LOGGER_CONFIG from obnb.alltypes import List, LogLevel, Optional, Union +from obnb.config.logger_config import LOGGER_CONFIG def verbose(level: Union[int, str], threshold="INFO") -> bool: 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/resolver.py b/src/obnb/util/resolver.py index fdeeb3c0..a0a8527a 100644 --- a/src/obnb/util/resolver.py +++ b/src/obnb/util/resolver.py @@ -1,8 +1,8 @@ import warnings from pprint import pformat -from obnb.registry import REGISTRIES from obnb.alltypes import Any, Dict, Optional, Union +from obnb.registry import REGISTRIES def resolve_registry(name: str, scope: Optional[str] = None, verbose: bool = True): diff --git a/src/obnb/util/version.py b/src/obnb/util/version.py index 13e31084..268e8539 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.alltypes import List