├── .bumpversion.cfg ├── .gitattributes ├── .github ├── dependabot.yml └── workflows │ ├── examples.yml │ ├── examples_latest.yml │ ├── release.yml │ ├── test_data.yml │ └── tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .yamllint.yml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── requirements.txt └── source │ ├── api │ ├── obnb.data.rst │ ├── obnb.feature.rst │ ├── obnb.graph.rst │ ├── obnb.label.rst │ ├── obnb.metric.rst │ └── obnb.model_trainer.rst │ ├── conf.py │ └── index.rst ├── example ├── eval_and_predict.py ├── example_config.yaml ├── filter_by_split.py ├── gcn_studybias_holdout.py ├── graphgym_studybias_holdout.py ├── label_propagation_studybias_holdout.py ├── logistic_regression_studybias_holdout.py ├── n2v_hypertune_studybias_holdout.py ├── negative_selection.py ├── parallel.py ├── run_all.sh ├── sample_classification.py ├── sl_predict.py ├── training │ ├── gnn_dgl.py │ └── gnn_pyg.py └── utils.py ├── install.sh ├── pyproject.toml ├── requirements.txt ├── script └── release_data.py ├── setup.py ├── src └── obnb │ ├── __init__.py │ ├── alltypes.py │ ├── config │ ├── __init__.py │ └── logger_config.py │ ├── data │ ├── __init__.py │ ├── annotated_ontology │ │ ├── __init__.py │ │ ├── base.py │ │ ├── diseases.py │ │ ├── disgenet.py │ │ ├── go.py │ │ └── hpo.py │ ├── annotation │ │ ├── __init__.py │ │ ├── base.py │ │ ├── diseases.py │ │ ├── disgenet.py │ │ ├── gene_ontology.py │ │ └── human_phenotype_ontology.py │ ├── base.py │ ├── experimental │ │ ├── __init__.py │ │ └── alevinfry.py │ ├── network │ │ ├── __init__.py │ │ ├── base.py │ │ ├── biogrid.py │ │ ├── bioplex.py │ │ ├── comppi.py │ │ ├── consensuspathdb.py │ │ ├── funcoup.py │ │ ├── hippie.py │ │ ├── humanbase.py │ │ ├── humannet.py │ │ ├── humap.py │ │ ├── huri.py │ │ ├── omnipath.py │ │ ├── pcnet.py │ │ ├── proteomehd.py │ │ ├── signor.py │ │ └── stringprot.py │ └── ontology │ │ ├── __init__.py │ │ ├── base.py │ │ ├── gene_ontology.py │ │ └── mondo.py │ ├── dataset │ ├── __init__.py │ ├── base.py │ ├── dataset.py │ ├── dataset_dgl.py │ └── dataset_pyg.py │ ├── exception.py │ ├── ext │ ├── __init__.py │ ├── attnwalk.py │ ├── grape.py │ ├── orbital_features.py │ ├── pecanpy.py │ └── sknetwork.py │ ├── feature │ ├── __init__.py │ ├── base.py │ ├── multifeat.py │ └── singlefeat.py │ ├── graph │ ├── __init__.py │ ├── base.py │ ├── dense.py │ ├── ontology.py │ └── sparse.py │ ├── label │ ├── __init__.py │ ├── collection.py │ ├── filters │ │ ├── __init__.py │ │ ├── base.py │ │ ├── existence_filter.py │ │ ├── negative_generator.py │ │ ├── nonred.py │ │ ├── pairwise_filter.py │ │ ├── range_filter.py │ │ └── value_filter.py │ └── split │ │ ├── __init__.py │ │ ├── base.py │ │ ├── holdout.py │ │ └── partition.py │ ├── metric │ ├── __init__.py │ ├── graphgym_metric.py │ └── standard.py │ ├── model │ ├── __init__.py │ └── label_propagation.py │ ├── model_trainer │ ├── __init__.py │ ├── base.py │ ├── gnn.py │ ├── graphgym.py │ ├── label_propagation.py │ └── supervised_learning.py │ ├── registry.py │ ├── transform │ ├── __init__.py │ ├── base.py │ └── node_feature.py │ └── util │ ├── __init__.py │ ├── checkers.py │ ├── converter.py │ ├── cx_explorer.py │ ├── deprecated.py │ ├── download.py │ ├── idhandler.py │ ├── io.py │ ├── logger.py │ ├── misc.py │ ├── parallel.py │ ├── path.py │ ├── registers.py │ ├── resolver.py │ ├── timer.py │ └── version.py ├── test ├── commonvar.py ├── conftest.py ├── data │ ├── experimental │ │ ├── __init__.py │ │ └── test_alevinfry.py │ ├── test_annotated_ontology.py │ ├── test_annotation.py │ ├── test_download.py │ └── test_ontology.py ├── ext │ ├── attnwalk.py │ ├── conftest.py │ ├── test_grape.py │ ├── test_orbital_features.py │ ├── test_pecanpy.py │ └── test_sknetwork.py ├── feature │ ├── __init__.py │ ├── test_align.py │ ├── test_multifeat.py │ └── test_singlefeat.py ├── graph │ ├── __init__.py │ ├── test_degree.py │ ├── test_directed_sparse_graph.py │ └── test_get_neighbors.py ├── sample_data │ ├── toy1.emd │ ├── toy1.gmt │ ├── toy1_property.tsv │ ├── toy1_unweighted.edg │ ├── toy1_weighted.edg │ └── toy_ontology.obo ├── test_data.py ├── test_dataset.py ├── test_graph.py ├── test_label │ ├── filters │ │ ├── __init__.py │ │ └── test_nonred.py │ ├── test_filter.py │ ├── test_labelset_collection.py │ └── test_split.py ├── test_metric.py ├── test_model.py ├── test_util │ ├── test_checkers.py │ ├── test_converter.py │ ├── test_idlst.py │ ├── test_idmap.py │ ├── test_idprop.py │ └── test_timer.py ├── test_wrapper.py ├── transform │ └── node_feature.py └── util │ └── checkers │ ├── __init__.py │ ├── test_check_config.py │ └── test_check_values.py ├── tox.ini └── tutorials └── basic_tutorial.ipynb /.bumpversion.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/krishnanlab/obnb/HEAD/.bumpversion.cfg 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