omnigenome 0.3.1a0__py3-none-any.whl → 0.4.0a0__py3-none-any.whl

omnigenome/__init__.py

@@ -1,266 +1,304 @@
-# -*- coding: utf-8 -*-
-# file: __init__.py
-# time: 14:53 06/04/2024
-# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
-# github: https://github.com/yangheng95
-# huggingface: https://huggingface.co/yangheng
-# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
-# Copyright (C) 2019-2024. All Rights Reserved.
-
-"""
-This __init__.py file exposes the Key API Entries of the library for easy access.
-Use dir(omnigenome) to see all available APIs.
-
-Key API Entries:
-----------------
-- AutoBench: Automated benchmarking of genomic models
-- AutoTrain: Automated training of genomic models
-- BenchHub: Hub for accessing benchmarks
-- ModelHub: Hub for accessing pre-trained models
-- PipelineHub: Hub for accessing pipelines
-- Various model classes for different genomic tasks
-- Dataset classes for different data formats
-- Tokenizer classes for different sequence representations
-- Metric classes for evaluation
-- Trainer classes for model training
-"""
-
-__name__ = "omnigenbench"
-__version__ = "0.3.1alpha"
-
-__author__ = "YANG, HENG"
-__email__ = "yangheng2021@gmail.com"
-__license__ = "Apache-2.0"
-
-# Import core auto components
-from .auto.auto_bench.auto_bench import AutoBench
-from .auto.auto_bench.auto_bench_config import AutoBenchConfig
-from .auto.bench_hub.bench_hub import BenchHub
-from .auto.auto_train.auto_train import AutoTrain
-from .auto.auto_bench.auto_bench_cli import run_bench, bench_command
-from .auto.auto_train.auto_train_cli import run_train, train_command
-
-# Import source modules
-from .src import dataset as dataset
-from .src import metric as metric
-from .src import model as model
-from .src import tokenizer as tokenizer
-
-# Import abstract base classes
-from .src.abc.abstract_dataset import OmniDataset
-from .src.abc.abstract_metric import OmniMetric
-from .src.abc.abstract_model import OmniModel
-from .src.abc.abstract_tokenizer import OmniTokenizer
-from .src.abc.abstract_tokenizer import OmniTokenizer as AutoTokenizer
-
-# Import dataset classes
-from .src.dataset.omni_dataset import OmniDatasetForSequenceClassification
-from .src.dataset.omni_dataset import OmniDatasetForSequenceRegression
-from .src.dataset.omni_dataset import OmniDatasetForTokenClassification
-from .src.dataset.omni_dataset import OmniDatasetForTokenRegression
-
-# Import metric classes
-from .src.metric import ClassificationMetric, RegressionMetric, RankingMetric
-
-# Import utility functions
-from .src.misc import utils as utils
-from .src.misc.utils import clean_temp_dir_pt_files
-
-# Import model classes
-from .src.model import (
-    OmniModelForSequenceClassification,
-    OmniModelForMultiLabelSequenceClassification,
-    OmniModelForTokenClassification,
-    OmniModelForSequenceRegression,
-    OmniModelForTokenRegression,
-    OmniModelForStructuralImputation,
-    OmniModelForMatrixRegression,
-    OmniModelForMatrixClassification,
-    OmniModelForMLM,
-    OmniModelForSeq2Seq,
-    OmniModelForRNADesign,
-    OmniModelForEmbedding,
-    OmniModelForAugmentation,
-)
-
-# Import LoRA model
-from .src.lora.lora_model import OmniLoraModel
-
-# Import tokenizer classes
-from .src.tokenizer import OmniBPETokenizer
-from .src.tokenizer import OmniKmersTokenizer
-from .src.tokenizer import OmniSingleNucleotideTokenizer
-
-# Import trainer classes
-from .src.trainer.hf_trainer import HFTrainer
-from .src.trainer.trainer import Trainer
-from .src.trainer.accelerate_trainer import AccelerateTrainer
-
-# Import hub utilities
-from .utility.hub_utils import download_benchmark
-from .utility.hub_utils import download_model
-from .utility.hub_utils import download_pipeline
-from .utility import hub_utils as hub_utils
-
-# Import hub classes
-from .utility.model_hub.model_hub import ModelHub
-from .utility.dataset_hub.dataset_hub import load_benchmark_datasets
-from .utility.pipeline_hub.pipeline import Pipeline
-from .utility.pipeline_hub.pipeline_hub import PipelineHub
-
-# Import module utilities
-from .src.model.module_utils import OmniPooling
-
-# --------------------------------------------------------------------------------
-# For backward compatibility version 0.2.7alpha and earlier
-from .src.abc.abstract_tokenizer import OmniTokenizer as OmniGenomeTokenizer
-from .src.abc.abstract_dataset import OmniDataset as OmniGenomeDataset
-from .src.abc.abstract_metric import OmniMetric as OmniGenomeMetric
-from .src.abc.abstract_model import OmniModel as OmniGenomeModel
-from .src.dataset.omni_dataset import (
-    OmniDatasetForSequenceClassification as OmniGenomeDatasetForSequenceClassification,
-)
-from .src.dataset.omni_dataset import (
-    OmniDatasetForSequenceRegression as OmniGenomeDatasetForSequenceRegression,
-)
-from .src.dataset.omni_dataset import (
-    OmniDatasetForTokenClassification as OmniGenomeDatasetForTokenClassification,
-)
-from .src.dataset.omni_dataset import (
-    OmniDatasetForTokenRegression as OmniGenomeDatasetForTokenRegression,
-)
-from .src.lora.lora_model import OmniLoraModel as OmniGenomeLoraModel
-from .src.model import (
-    OmniModelForSequenceClassification as OmniGenomeModelForSequenceClassification,
-    OmniModelForMultiLabelSequenceClassification as OmniGenomeModelForMultiLabelSequenceClassification,
-    OmniModelForTokenClassification as OmniGenomeModelForTokenClassification,
-    OmniModelForSequenceRegression as OmniGenomeModelForSequenceRegression,
-    OmniModelForTokenRegression as OmniGenomeModelForTokenRegression,
-    OmniModelForStructuralImputation as OmniGenomeModelForStructuralImputation,
-    OmniModelForMatrixRegression as OmniGenomeModelForMatrixRegression,
-    OmniModelForMatrixClassification as OmniGenomeModelForMatrixClassification,
-    OmniModelForMLM as OmniGenomeModelForMLM,
-    OmniModelForSeq2Seq as OmniGenomeModelForSeq2Seq,
-    OmniModelForRNADesign as OmniGenomeModelForRNADesign,
-    OmniModelForEmbedding as OmniGenomeModelForEmbedding,
-    OmniModelForAugmentation as OmniGenomeModelForAugmentation,
-)
-
-from .utility.ensemble import VoteEnsemblePredictor
-
-# ------------------------------------------------------------------------------
-
-
-__all__ = [
-    "load_benchmark_datasets",
-    "OmniDataset",
-    "OmniModel",
-    "OmniMetric",
-    "AutoTokenizer",
-    "OmniTokenizer",
-    "OmniKmersTokenizer",
-    "OmniSingleNucleotideTokenizer",
-    "OmniBPETokenizer",
-    "ModelHub",
-    "Pipeline",
-    "PipelineHub",
-    "BenchHub",
-    "AutoBench",
-    "AutoBenchConfig",
-    "utils",
-    "model",
-    "tokenizer",
-    "dataset",
-    "OmniModelForSequenceClassification",
-    "OmniModelForMultiLabelSequenceClassification",
-    "OmniModelForTokenClassification",
-    "OmniModelForSequenceRegression",
-    "OmniModelForTokenRegression",
-    "OmniModelForRNADesign",
-    "OmniModelForEmbedding",
-    "OmniModelForAugmentation",
-    "OmniModelForStructuralImputation",
-    "OmniModelForMatrixRegression",
-    "OmniModelForMatrixClassification",
-    "OmniModelForMLM",
-    "OmniModelForSeq2Seq",
-    "OmniDatasetForTokenClassification",
-    "OmniDatasetForTokenRegression",
-    "OmniDatasetForSequenceClassification",
-    "OmniDatasetForSequenceRegression",
-    "OmniLoraModel",
-    "ClassificationMetric",
-    "RegressionMetric",
-    "RankingMetric",
-    "Trainer",
-    "HFTrainer",
-    "AccelerateTrainer",
-    "AutoBenchConfig",
-    "AutoBench",
-    "download_benchmark",
-    "download_model",
-    "download_pipeline",
-    "VoteEnsemblePredictor",
-]
-
-
-LOGO1 = r"""                       
-    **@@ #========= @@**            ___                     _ 
-      **@@ +----- @@**             / _ \  _ __ ___   _ __  (_)
-        **@@ = @@**               | | | || '_ ` _ \ | '_ \ | |
-           **@@                   | |_| || | | | | || | | || |
-        @@** = **@@                \___/ |_| |_| |_||_| |_||_|
-     @@** ------+ **@@                
-   @@** =========# **@@            ____  
-  @@ ---------------+ @@          / ___|  ___  _ __   
- @@ ================== @@        | |  _  / _ \| '_ \
-  @@ +--------------- @@         | |_| ||  __/| | | |
-   @@** #========= **@@           \____| \___||_| |_| 
-    @@** +------ **@@          
-       @@** = **@@           
-          @@**                    ____                      _   
-       **@@ = @@**               | __ )   ___  _ __    ___ | |__  
-    **@@ -----+  @@**            |  _ \  / _ \| '_ \  / __|| '_ \ 
-  **@@ ==========# @@**          | |_) ||  __/| | | || (__ | | | |
-  @@ --------------+ @@**        |____/  \___||_| |_| \___||_| |_|
-"""
-
-LOGO2 = r"""
-
-   **  +----------- **           ___                     _ 
-  @@                 @@         / _ \  _ __ ___   _ __  (_)
- @@* #============== *@@       | | | || '_ ` _ \ | '_ \ | |
- @@*                 *@@       | |_| || | | | | || | | || |
- *@@  +------------ *@@         \___/ |_| |_| |_||_| |_||_|
-  *@*               @@*       
-   *@@  #========= @@*        
-    *@@*         *@@*          
-      *@@  +---@@@*              ____  
-        *@@*   **               / ___|  ___  _ __  
-          **@**                | |  _  / _ \| '_ \ 
-        *@@* *@@*              | |_| ||  __/| | | |
-      *@@ ---+  @@*             \____| \___||_| |_|
-    *@@*         *@@*          
-   *@@ =========#  @@*         
-  *@@               @@*        
- *@@ -------------+  @@*        ____                      _   
- @@                   @@       | __ )   ___  _ __    ___ | |__ 
- @@ ===============#  @@       |  _ \  / _ \| '_ \  / __|| '_ \ 
-  @@                 @@        | |_) ||  __/| | | || (__ | | | |
-   ** -----------+  **         |____/  \___||_| |_| \___||_| |_|
-"""
-
-art_dna_color_map = {
-    "*": "blue",  # Bases represented by '*'
-    "@": "white",  # Bases represented by '@'
-    "-": "yellow",  # Hydrogen bonds, assuming '-' represents a bond
-    "=": "light_cyan",  # Hydrogen bonds, assuming '=' represents a bond
-    "+": "yellow",  # '+' symbols in cyan
-    " ": "black",  # Use red for undefined characters
-}
-import random
-
-LOGO = random.choice([LOGO1, LOGO2])
-print(LOGO)
-
-clean_temp_dir_pt_files()
+# -*- coding: utf-8 -*-
+# file: __init__.py
+# time: 14:53 06/04/2024
+# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
+# github: https://github.com/yangheng95
+# huggingface: https://huggingface.co/yangheng
+# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
+# Copyright (C) 2019-2024. All Rights Reserved.
+
+"""
+OmniGenome - Alias package for omnigenbench
+===========================================
+
+This package provides the same functionality as omnigenbench but with the omnigenome name.
+All imports are redirected to the omnigenbench package.
+
+For backward compatibility, this package maintains the same API as omnigenbench.
+"""
+from omnigenbench import __version__
+
+# Package metadata (define locally to avoid circular imports)
+__name__ = "omnigenome"
+__version__ = __version__
+__author__ = "Yang, Heng"
+__email__ = "yangheng2021@gmail.com"
+__license__ = "Apache-2.0"
+
+import warnings
+
+warnings.warn(
+    "The 'omnigenome' package is deprecated, please use omnigenbench package instead. "
+    "e.g., from omnigenbench import *  ->  from omnigenbench import *\n"
+    "All imports from omnigenome will be redirected to omnigenbench. ",
+    DeprecationWarning,
+)
+
+# Import strategy: Try to import from omnigenbench with proper error handling
+try:
+    # Import core auto components
+    from omnigenbench.auto.auto_bench.auto_bench import AutoBench
+    from omnigenbench.auto.config.auto_config import AutoConfig
+    from omnigenbench.auto.bench_hub.bench_hub import BenchHub
+    from omnigenbench.auto.auto_train.auto_train import AutoTrain
+    from omnigenbench.auto.auto_bench.auto_bench_cli import run_bench, bench_command
+    from omnigenbench.auto.auto_train.auto_train_cli import run_train, train_command
+
+    # Import source modules
+    from omnigenbench.src import dataset, metric, model, tokenizer
+
+    # Import abstract base classes
+    from omnigenbench.src.abc.abstract_dataset import OmniDataset
+    from omnigenbench.src.abc.abstract_metric import OmniMetric
+    from omnigenbench.src.abc.abstract_model import OmniModel
+    from omnigenbench.src.abc.abstract_tokenizer import OmniTokenizer
+
+    # Import dataset classes
+    from omnigenbench.src.dataset.omni_dataset import (
+        OmniDatasetForSequenceClassification,
+        OmniDatasetForSequenceRegression,
+        OmniDatasetForTokenClassification,
+        OmniDatasetForTokenRegression,
+        OmniDatasetForMultiLabelClassification,
+    )
+
+    # Import metric classes
+    from omnigenbench.src.metric import (
+        ClassificationMetric,
+        RegressionMetric,
+        RankingMetric,
+    )
+
+    # Import utility functions
+    from omnigenbench.src.misc.utils import (
+        clean_temp_dir_pt_files,
+        fprint,
+        seed_everything,
+        save_args,
+        naive_secondary_structure_repair,
+        check_bench_version,
+        clean_temp_checkpoint,
+        print_args,
+        env_meta_info,
+        RNA2StructureCache,
+    )
+
+    # Import model classes
+    from omnigenbench.src.model import (
+        OmniModelForSequenceClassification,
+        OmniModelForMultiLabelSequenceClassification,
+        OmniModelForTokenClassification,
+        OmniModelForSequenceRegression,
+        OmniModelForTokenRegression,
+        OmniModelForStructuralImputation,
+        OmniModelForMatrixRegression,
+        OmniModelForMatrixClassification,
+        OmniModelForMLM,
+        OmniModelForSeq2Seq,
+        OmniModelForRNADesign,
+        OmniModelForEmbedding,
+        OmniModelForAugmentation,
+    )
+
+    from omnigenbench.src.model.baselines import (
+        OmniCNNBaseline,
+        OmniRNNBaseline,
+        OmniBPNetBaseline,
+        OmniBasenjiBaseline,
+        OmniDeepSTARRBaseline,
+        OmniGenericBaseline,
+    )
+
+    # Import LoRA model
+    from omnigenbench.src.lora.lora_model import OmniLoraModel
+
+    # Import tokenizer classes
+    from omnigenbench.src.tokenizer import (
+        OmniBPETokenizer,
+        OmniKmersTokenizer,
+        OmniSingleNucleotideTokenizer,
+    )
+
+    # Import trainer classes
+    from omnigenbench.src.trainer.hf_trainer import HFTrainer
+    from omnigenbench.src.trainer.trainer import Trainer
+    from omnigenbench.src.trainer.accelerate_trainer import AccelerateTrainer
+
+    # Import hub utilities
+    from omnigenbench.src.utility.hub_utils import (
+        download_benchmark,
+        download_model,
+        download_pipeline,
+        query_models_info,
+    )
+    from omnigenbench.src.utility import hub_utils
+
+    # Import hub classes
+    from omnigenbench.src.utility.model_hub.model_hub import ModelHub
+    from omnigenbench.src.utility.dataset_hub.dataset_hub import load_benchmark_datasets
+    from omnigenbench.src.utility.pipeline_hub.pipeline import Pipeline
+    from omnigenbench.src.utility.pipeline_hub.pipeline_hub import PipelineHub
+
+    # Import module utilities
+    from omnigenbench.src.model.module_utils import OmniPooling
+    from omnigenbench.src.utility.ensemble import VoteEnsemblePredictor
+
+    # For backward compatibility version 0.2.7alpha and earlier
+    from omnigenbench.auto.config.auto_config import AutoBenchConfig
+
+    # Import explainer classes
+    from omnigenbench.src.explainability.epistasis.explainer import EpistasisExplainer
+    from omnigenbench.src.explainability.sequence_logo.explainer import (
+        SequenceLogoExplainer,
+    )
+    from omnigenbench.src.explainability.visualization_2d.explainer import (
+        Visualization2DExplainer,
+    )
+    from omnigenbench.src.explainability.attention.explainer import AttentionExplainer
+
+    # Create backward compatibility aliases
+    OmniGenomeTokenizer = OmniTokenizer
+    OmniGenomeKmersTokenizer = OmniKmersTokenizer
+    OmniGenomeSingleNucleotideTokenizer = OmniSingleNucleotideTokenizer
+    OmniGenomeBPETokenizer = OmniBPETokenizer
+    OmniGenomeDataset = OmniDataset
+    OmniGenomeMetric = OmniMetric
+    OmniGenomeModel = OmniModel
+    OmniGenomeDatasetForSequenceClassification = OmniDatasetForSequenceClassification
+    OmniGenomeDatasetForSequenceRegression = OmniDatasetForSequenceRegression
+    OmniGenomeDatasetForTokenClassification = OmniDatasetForTokenClassification
+    OmniGenomeDatasetForTokenRegression = OmniDatasetForTokenRegression
+    OmniGenomeLoraModel = OmniLoraModel
+    OmniGenomeModelForSequenceClassification = OmniModelForSequenceClassification
+    OmniGenomeModelForMultiLabelSequenceClassification = (
+        OmniModelForMultiLabelSequenceClassification
+    )
+    OmniGenomeModelForTokenClassification = OmniModelForTokenClassification
+    OmniGenomeModelForSequenceRegression = OmniModelForSequenceRegression
+    OmniGenomeModelForTokenRegression = OmniModelForTokenRegression
+    OmniGenomeModelForStructuralImputation = OmniModelForStructuralImputation
+    OmniGenomeModelForMatrixRegression = OmniModelForMatrixRegression
+    OmniGenomeModelForMatrixClassification = OmniModelForMatrixClassification
+    OmniGenomeModelForMLM = OmniModelForMLM
+    OmniGenomeModelForSeq2Seq = OmniModelForSeq2Seq
+    OmniGenomeModelForRNADesign = OmniModelForRNADesign
+    OmniGenomeModelForEmbedding = OmniModelForEmbedding
+    OmniGenomeModelForAugmentation = OmniModelForAugmentation
+
+    # Define __all__ for explicit exports
+    __all__ = [
+        "__version__",
+        "load_benchmark_datasets",
+        "OmniDataset",
+        "OmniModel",
+        "OmniMetric",
+        "OmniTokenizer",
+        "OmniKmersTokenizer",
+        "OmniSingleNucleotideTokenizer",
+        "OmniBPETokenizer",
+        "ModelHub",
+        "Pipeline",
+        "PipelineHub",
+        "BenchHub",
+        "AutoBench",
+        "AutoTrain",
+        "AutoConfig",
+        "ClassificationMetric",
+        "RegressionMetric",
+        "RankingMetric",
+        "Trainer",
+        "HFTrainer",
+        "AccelerateTrainer",
+        "AutoBenchConfig",
+        "download_benchmark",
+        "download_model",
+        "download_pipeline",
+        "VoteEnsemblePredictor",
+        "clean_temp_dir_pt_files",
+        "fprint",
+        "seed_everything",
+        "save_args",
+        "naive_secondary_structure_repair",
+        "check_bench_version",
+        "clean_temp_checkpoint",
+        "print_args",
+        "env_meta_info",
+        "RNA2StructureCache",
+        "OmniDatasetForSequenceClassification",
+        "OmniDatasetForSequenceRegression",
+        "OmniDatasetForTokenClassification",
+        "OmniDatasetForTokenRegression",
+        "OmniDatasetForMultiLabelClassification",
+        "OmniTokenizer",
+        "OmniKmersTokenizer",
+        "OmniSingleNucleotideTokenizer",
+        "OmniBPETokenizer",
+        "OmniDataset",
+        "OmniMetric",
+        "OmniModel",
+        "OmniLoraModel",
+        "OmniModelForSequenceClassification",
+        "OmniModelForMultiLabelSequenceClassification",
+        "OmniModelForTokenClassification",
+        "OmniModelForSequenceRegression",
+        "OmniModelForTokenRegression",
+        "OmniModelForStructuralImputation",
+        "OmniModelForMatrixRegression",
+        "OmniModelForMatrixClassification",
+        "OmniModelForMLM",
+        "OmniModelForSeq2Seq",
+        "OmniModelForRNADesign",
+        "OmniModelForEmbedding",
+        "OmniModelForAugmentation",
+        "OmniPooling",
+        "download_benchmark",
+        "download_model",
+        "download_pipeline",
+        "query_models_info",
+        "hub_utils",
+        "OmniCNNBaseline",
+        "OmniRNNBaseline",
+        "OmniBPNetBaseline",
+        "OmniBasenjiBaseline",
+        "OmniDeepSTARRBaseline",
+        "OmniGenericBaseline",
+        # OmniGenome* aliases for backward compatibility
+        "OmniGenomeTokenizer",
+        "OmniGenomeKmersTokenizer",
+        "OmniGenomeSingleNucleotideTokenizer",
+        "OmniGenomeBPETokenizer",
+        "OmniGenomeDataset",
+        "OmniGenomeMetric",
+        "OmniGenomeModel",
+        "OmniGenomeDatasetForSequenceClassification",
+        "OmniGenomeDatasetForSequenceRegression",
+        "OmniGenomeDatasetForTokenClassification",
+        "OmniGenomeDatasetForTokenRegression",
+        "OmniGenomeLoraModel",
+        "OmniGenomeModelForSequenceClassification",
+        "OmniGenomeModelForMultiLabelSequenceClassification",
+        "OmniGenomeModelForTokenClassification",
+        "OmniGenomeModelForSequenceRegression",
+        "OmniGenomeModelForTokenRegression",
+        "OmniGenomeModelForStructuralImputation",
+        "OmniGenomeModelForMatrixRegression",
+        "OmniGenomeModelForMatrixClassification",
+        "OmniGenomeModelForMLM",
+        "OmniGenomeModelForSeq2Seq",
+        "OmniGenomeModelForRNADesign",
+        "OmniGenomeModelForEmbedding",
+        "OmniGenomeModelForAugmentation",
+        # Command line functions
+        "run_bench",
+        "bench_command",
+        "run_train",
+        "train_command",
+        "EpistasisExplainer",
+        "SequenceLogoExplainer",
+        "Visualization2DExplainer",
+        "AttentionExplainer",
+    ]
+
+except ImportError as e:
+    # Minimal fallback to prevent complete failure
+    __all__ = []