omnigenome 0.0.1b0__tar.gz → 0.3.3a0__tar.gz

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@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: omnigenome
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- Version: 0.0.1b0
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+ Version: 0.3.3a0
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  Summary: OmniGenome: A comprehensive toolkit for genome analysis.
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  Home-page: https://github.com/yangheng95/OmniGenBench
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  Author: Yang, Heng
@@ -20,6 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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+ Requires-Dist: omnigenbench>=0.3.0
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  Requires-Dist: findfile>=2.0.0
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  Requires-Dist: autocuda>=0.16
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  Requires-Dist: metric-visualizer>=0.9.6
@@ -34,8 +35,6 @@ Requires-Dist: transformers>=4.46.0
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  Requires-Dist: packaging
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  Requires-Dist: peft
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  Requires-Dist: dill
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- Requires-Dist: accelerate
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- Requires-Dist: omnigenbench>=0.3.2alpha
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  Provides-Extra: dev
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  Requires-Dist: dill; extra == "dev"
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  Requires-Dist: pytest; extra == "dev"
@@ -0,0 +1,252 @@
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+ # -*- coding: utf-8 -*-
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+ # file: __init__.py
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+ # time: 14:53 06/04/2024
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+ # author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
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+ # github: https://github.com/yangheng95
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+ # huggingface: https://huggingface.co/yangheng
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+ # google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
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+ # Copyright (C) 2019-2024. All Rights Reserved.
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+
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+ """
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+ OmniGenome - Alias package for omnigenbench
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+ ===========================================
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+
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+ This package provides the same functionality as omnigenbench but with the omnigenome name.
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+ All imports are redirected to the omnigenbench package.
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+
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+ For backward compatibility, this package maintains the same API as omnigenbench.
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+ """
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+ from omnigenbench import __version__
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+
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+ # Package metadata (define locally to avoid circular imports)
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+ __name__ = "omnigenome"
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+ __version__ = __version__
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+ __author__ = "Yang, Heng"
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+ __email__ = "yangheng2021@gmail.com"
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+ __license__ = "Apache-2.0"
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+
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+ import warnings
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+
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+ warnings.warn(
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+ "The 'omnigenome' package is deprecated, please use omnigenbench package instead. "
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+ "e.g., from omnigenome import * -> from omnigenbench import *\n"
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+ "All imports from omnigenome will be redirected to omnigenbench. ",
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+ DeprecationWarning,
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+ )
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+
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+ # Import strategy: Try to import from omnigenbench with proper error handling
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+ try:
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+ # Import core auto components
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+ from omnigenbench.auto.auto_bench.auto_bench import AutoBench
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+ from omnigenbench.auto.config.auto_config import AutoConfig
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+ from omnigenbench.auto.bench_hub.bench_hub import BenchHub
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+ from omnigenbench.auto.auto_train.auto_train import AutoTrain
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+ from omnigenbench.auto.auto_bench.auto_bench_cli import run_bench, bench_command
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+ from omnigenbench.auto.auto_train.auto_train_cli import run_train, train_command
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+
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+ # Import source modules
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+ from omnigenbench.src import dataset, metric, model, tokenizer
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+
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+ # Import abstract base classes
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+ from omnigenbench.src.abc.abstract_dataset import OmniDataset
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+ from omnigenbench.src.abc.abstract_metric import OmniMetric
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+ from omnigenbench.src.abc.abstract_model import OmniModel
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+ from omnigenbench.src.abc.abstract_tokenizer import OmniTokenizer
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+
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+ # Import dataset classes
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+ from omnigenbench.src.dataset.omni_dataset import (
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+ OmniDatasetForSequenceClassification,
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+ OmniDatasetForSequenceRegression,
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+ OmniDatasetForTokenClassification,
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+ OmniDatasetForTokenRegression,
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+ )
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+
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+ # Import metric classes
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+ from omnigenbench.src.metric import (
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+ ClassificationMetric,
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+ RegressionMetric,
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+ RankingMetric,
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+ )
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+
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+ # Import utility functions
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+ from omnigenbench.src.misc.utils import (
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+ clean_temp_dir_pt_files,
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+ fprint,
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+ seed_everything,
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+ save_args,
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+ naive_secondary_structure_repair,
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+ check_bench_version,
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+ clean_temp_checkpoint,
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+ print_args,
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+ env_meta_info,
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+ RNA2StructureCache,
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+ )
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+
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+ # Import model classes
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+ from omnigenbench.src.model import (
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+ OmniModelForSequenceClassification,
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+ OmniModelForMultiLabelSequenceClassification,
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+ OmniModelForTokenClassification,
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+ OmniModelForSequenceRegression,
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+ OmniModelForTokenRegression,
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+ OmniModelForStructuralImputation,
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+ OmniModelForMatrixRegression,
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+ OmniModelForMatrixClassification,
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+ OmniModelForMLM,
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+ OmniModelForSeq2Seq,
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+ OmniModelForRNADesign,
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+ OmniModelForEmbedding,
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+ OmniModelForAugmentation,
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+ )
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+
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+ # Import LoRA model
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+ from omnigenbench.src.lora.lora_model import OmniLoraModel
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+
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+ # Import tokenizer classes
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+ from omnigenbench.src.tokenizer import (
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+ OmniBPETokenizer,
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+ OmniKmersTokenizer,
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+ OmniSingleNucleotideTokenizer,
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+ )
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+
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+ # Import trainer classes
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+ from omnigenbench.src.trainer.hf_trainer import HFTrainer
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+ from omnigenbench.src.trainer.trainer import Trainer
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+ from omnigenbench.src.trainer.accelerate_trainer import AccelerateTrainer
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+
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+ # Import hub utilities
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+ from omnigenbench.utility.hub_utils import (
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+ download_benchmark,
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+ download_model,
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+ download_pipeline,
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+ query_models_info,
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+ )
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+ from omnigenbench.utility import hub_utils
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+
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+ # Import hub classes
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+ from omnigenbench.utility.model_hub.model_hub import ModelHub
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+ from omnigenbench.utility.dataset_hub.dataset_hub import load_benchmark_datasets
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+ from omnigenbench.utility.pipeline_hub.pipeline import Pipeline
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+ from omnigenbench.utility.pipeline_hub.pipeline_hub import PipelineHub
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+
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+ # Import module utilities
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+ from omnigenbench.src.model.module_utils import OmniPooling
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+ from omnigenbench.utility.ensemble import VoteEnsemblePredictor
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+
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+ # For backward compatibility version 0.2.7alpha and earlier
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+ from omnigenbench.auto.config.auto_config import AutoBenchConfig
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+
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+ # Create backward compatibility aliases
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+ OmniGenomeTokenizer = OmniTokenizer
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+ OmniGenomeKmersTokenizer = OmniKmersTokenizer
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+ OmniGenomeSingleNucleotideTokenizer = OmniSingleNucleotideTokenizer
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+ OmniGenomeBPETokenizer = OmniBPETokenizer
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+ OmniGenomeDataset = OmniDataset
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+ OmniGenomeMetric = OmniMetric
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+ OmniGenomeModel = OmniModel
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+ OmniGenomeDatasetForSequenceClassification = OmniDatasetForSequenceClassification
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+ OmniGenomeDatasetForSequenceRegression = OmniDatasetForSequenceRegression
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+ OmniGenomeDatasetForTokenClassification = OmniDatasetForTokenClassification
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+ OmniGenomeDatasetForTokenRegression = OmniDatasetForTokenRegression
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+ OmniGenomeLoraModel = OmniLoraModel
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+ OmniGenomeModelForSequenceClassification = OmniModelForSequenceClassification
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+ OmniGenomeModelForMultiLabelSequenceClassification = (
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+ OmniModelForMultiLabelSequenceClassification
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+ )
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+ OmniGenomeModelForTokenClassification = OmniModelForTokenClassification
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+ OmniGenomeModelForSequenceRegression = OmniModelForSequenceRegression
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+ OmniGenomeModelForTokenRegression = OmniModelForTokenRegression
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+ OmniGenomeModelForStructuralImputation = OmniModelForStructuralImputation
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+ OmniGenomeModelForMatrixRegression = OmniModelForMatrixRegression
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+ OmniGenomeModelForMatrixClassification = OmniModelForMatrixClassification
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+ OmniGenomeModelForMLM = OmniModelForMLM
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+ OmniGenomeModelForSeq2Seq = OmniModelForSeq2Seq
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+ OmniGenomeModelForRNADesign = OmniModelForRNADesign
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+ OmniGenomeModelForEmbedding = OmniModelForEmbedding
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+ OmniGenomeModelForAugmentation = OmniModelForAugmentation
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+
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+ # Define __all__ for explicit exports
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+ __all__ = [
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+ "load_benchmark_datasets",
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+ "OmniDataset",
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+ "OmniModel",
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+ "OmniMetric",
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+ "OmniTokenizer",
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+ "OmniKmersTokenizer",
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+ "OmniSingleNucleotideTokenizer",
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+ "OmniBPETokenizer",
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+ "ModelHub",
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+ "Pipeline",
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+ "PipelineHub",
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+ "BenchHub",
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+ "AutoBench",
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+ "AutoTrain",
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+ "AutoConfig",
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+ "ClassificationMetric",
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+ "RegressionMetric",
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+ "RankingMetric",
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+ "Trainer",
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+ "HFTrainer",
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+ "AccelerateTrainer",
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+ "AutoBenchConfig",
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+ "download_benchmark",
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+ "download_model",
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+ "download_pipeline",
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+ "VoteEnsemblePredictor",
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+ "clean_temp_dir_pt_files",
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+ "fprint",
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+ "seed_everything",
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+ "save_args",
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+ "naive_secondary_structure_repair",
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+ "check_bench_version",
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+ "clean_temp_checkpoint",
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+ "print_args",
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+ "env_meta_info",
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+ "RNA2StructureCache",
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+ # OmniGenome* aliases for backward compatibility
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+ "OmniGenomeTokenizer",
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+ "OmniGenomeKmersTokenizer",
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+ "OmniGenomeSingleNucleotideTokenizer",
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+ "OmniGenomeBPETokenizer",
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+ "OmniGenomeDataset",
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+ "OmniGenomeMetric",
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+ "OmniGenomeModel",
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+ "OmniGenomeDatasetForSequenceClassification",
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+ "OmniGenomeDatasetForSequenceRegression",
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+ "OmniGenomeDatasetForTokenClassification",
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+ "OmniGenomeDatasetForTokenRegression",
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+ "OmniGenomeLoraModel",
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+ "OmniGenomeModelForSequenceClassification",
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+ "OmniGenomeModelForMultiLabelSequenceClassification",
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+ "OmniGenomeModelForTokenClassification",
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+ "OmniGenomeModelForSequenceRegression",
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+ "OmniGenomeModelForTokenRegression",
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+ "OmniGenomeModelForStructuralImputation",
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+ "OmniGenomeModelForMatrixRegression",
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+ "OmniGenomeModelForMatrixClassification",
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+ "OmniGenomeModelForMLM",
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+ "OmniGenomeModelForSeq2Seq",
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+ "OmniGenomeModelForRNADesign",
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+ "OmniGenomeModelForEmbedding",
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+ "OmniGenomeModelForAugmentation",
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+ # Command line functions
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+ "run_bench",
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+ "bench_command",
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+ "run_train",
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+ "train_command",
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+ ]
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+
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+ except ImportError as e:
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+ import warnings
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+
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+ warnings.warn(
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+ f"Failed to import omnigenbench modules: {e}. "
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+ "Please ensure omnigenbench is properly installed.\n"
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+ "You can install it with: pip install omnigenbench\n"
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+ "and replace all 'omnigenome' with 'omnigenbench' in your code.\n"
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+ "e.g., from omnigenome import * -> from omnigenbench import *",
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+ ImportWarning,
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+ )
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+
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+ # Minimal fallback to prevent complete failure
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+ __all__ = []
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: omnigenome
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- Version: 0.0.1b0
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+ Version: 0.3.3a0
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  Summary: OmniGenome: A comprehensive toolkit for genome analysis.
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  Home-page: https://github.com/yangheng95/OmniGenBench
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  Author: Yang, Heng
@@ -20,6 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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+ Requires-Dist: omnigenbench>=0.3.0
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  Requires-Dist: findfile>=2.0.0
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  Requires-Dist: autocuda>=0.16
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  Requires-Dist: metric-visualizer>=0.9.6
@@ -34,8 +35,6 @@ Requires-Dist: transformers>=4.46.0
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  Requires-Dist: packaging
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  Requires-Dist: peft
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  Requires-Dist: dill
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- Requires-Dist: accelerate
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- Requires-Dist: omnigenbench>=0.3.2alpha
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  Provides-Extra: dev
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  Requires-Dist: dill; extra == "dev"
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  Requires-Dist: pytest; extra == "dev"
@@ -5,6 +5,7 @@ omnigenome/__init__.py
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  omnigenome.egg-info/PKG-INFO
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  omnigenome.egg-info/SOURCES.txt
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  omnigenome.egg-info/dependency_links.txt
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+ omnigenome.egg-info/entry_points.txt
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  omnigenome.egg-info/requires.txt
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  omnigenome.egg-info/top_level.txt
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  tests/test_dataset_patterns.py
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+ [console_scripts]
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+ autobench = omnigenome:run_bench
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+ autotrain = omnigenome:run_train
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+ omnigenbench>=0.3.0
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  findfile>=2.0.0
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  autocuda>=0.16
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  metric-visualizer>=0.9.6
@@ -12,8 +13,6 @@ transformers>=4.46.0
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  packaging
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  peft
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  dill
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- accelerate
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- omnigenbench>=0.3.2alpha
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  [dev]
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  dill
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  from pathlib import Path
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  from setuptools import setup, find_packages
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+
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+ # Define version directly to avoid circular import
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  from omnigenome import __version__
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  cwd = Path(__file__).parent
@@ -37,9 +39,13 @@ setup(
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  license="Apache-2.0",
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  packages=find_packages(include=["omnigenome", "omnigenome.*"]),
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  entry_points={
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-
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+ "console_scripts": [
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+ "autobench=omnigenome:run_bench",
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+ "autotrain=omnigenome:run_train",
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+ ],
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  },
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  install_requires=[
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+ "omnigenbench>=0.3.0", # Add dependency on omnigenbench
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  "findfile>=2.0.0",
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  "autocuda>=0.16",
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  "metric-visualizer>=0.9.6",
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  "packaging",
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  "peft",
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  "dill",
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- "accelerate",
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- "omnigenbench>=0.3.2alpha", # Depend on the alias package
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  ],
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  extras_require=extras,
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  classifiers=[
@@ -1,26 +0,0 @@
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- # -*- coding: utf-8 -*-
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- # file: __init__.py
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- # time: 14:53 06/04/2024
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- # author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
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- # github: https://github.com/yangheng95
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- # huggingface: https://huggingface.co/yangheng
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- # google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
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- # Copyright (C) 2019-2024. All Rights Reserved.
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-
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- """
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- OmniGenBench - Alias package for omnigenome
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- ============================================
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-
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- This package provides the same functionality as omnigenome but with the omnigenbench name.
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- All imports are redirected to the omnigenome package.
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- """
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-
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- # Import everything from omnigenome to maintain compatibility
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- from omnigenbench import *
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-
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- # Override package metadata to reflect omnigenbench
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- __name__ = "omnigenome"
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- __version__ = "0.0.1beta"
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- __author__ = "Yang, Heng"
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- __email__ = "yangheng2021@gmail.com"
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- __license__ = "Apache-2.0"
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