omnigenome 0.3.1a0__tar.gz → 0.3.3a0__tar.gz

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.1a0
+Version: 0.3.3a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng
@@ -20,6 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: omnigenbench>=0.3.0
 Requires-Dist: findfile>=2.0.0
 Requires-Dist: autocuda>=0.16
 Requires-Dist: metric-visualizer>=0.9.6
@@ -34,7 +35,6 @@ Requires-Dist: transformers>=4.46.0
 Requires-Dist: packaging
 Requires-Dist: peft
 Requires-Dist: dill
-Requires-Dist: accelerate
 Provides-Extra: dev
 Requires-Dist: dill; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
@@ -54,7 +54,7 @@ Dynamic: summary
 
 ![favicon.png](asset/favicon.png)
 
-<h3 align="center">OmniGenBench is a modular benchmarking platform for evaluating genomic foundation models (GFMs) across diverse tasks like RNA structure prediction, gene function classification, and multi-species generalization.</h3>
+<h3 align="center">OmniGenBench offers an all-in-one solution for genomic foundation model finetuning, inference, deployment and automated benchmarking, designed for research and applications in genomics.</h3>
 
 <div align="center">
 
@@ -104,15 +104,15 @@ Dynamic: summary
 ## Installation
 
 ### Requirements
-Before installing OmniGenome, you need to install the following dependencies:
+Before installing OmniGenoBench, you need to install the following dependencies:
 - Python 3.10+
 - PyTorch 2.5+
 - Transformers 4.46.0+
 
 ### PyPI Installation
-To install OmniGenome, you can use pip:
+To install OmniGenoBench, you can use pip:
 ```bash
-pip install omnigenome -U
+pip install omnigenbench -U
 ```
 
 ### Source Installation
@@ -136,7 +136,7 @@ You can find a visualization of AutoBench [here](asset/AutoBench.gif).
 ### Auto-benchmark via Python API
 Or you can use the following python code to run the auto-benchmark:
 ```python
-from omnigenome import AutoBench
+from omnigenbench import AutoBench
 gfm = 'LongSafari/hyenadna-medium-160k-seqlen-hf'
 # benchmark could be "RGB", "GB", "PGB", "GUE", which will be downloaded from the Hugging Face model hub
 benchmark = "RGB"
@@ -185,7 +185,7 @@ OmniGenBench supports five curated benchmark suites covering both **sequence-lev
 ### RNA Design
 RNA design is a fundamental problem in synthetic biology,
 where the goal is to design RNA sequences that fold into a target structure.
-In this demo, we show how to use OmniGenome to design RNA sequences 
+In this demo, we show how to use OmniGenoBench to design RNA sequences 
 that fold into a target structure using a pre-trained model.
 The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_design/RNA_Design_Tutorial.ipynb).
 
@@ -195,7 +195,7 @@ You can find a visual example of RNA Design [here](asset/RNA_Design.gif).
 
 RNA secondary structure prediction is a fundamental problem in computational biology,
 where the goal is to predict the secondary structure of an RNA sequence.
-In this demo, we show how to use OmniGenome to predict the secondary structure of RNA sequences using a pre-trained model.
+In this demo, we show how to use OmniGenoBench to predict the secondary structure of RNA sequences using a pre-trained model.
 The tutorials of RNA Secondary Structure Prediction can be found in
 [Secondary_Structure_Prediction_Tutorial.ipynb](examples/rna_secondary_structure_prediction/Secondary_Structure_Prediction_Tutorial.ipynb).
 

omnigenome-0.3.3a0/omnigenome/__init__.py

@@ -0,0 +1,252 @@
+# -*- 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 omnigenome 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,
+    )
+
+    # 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,
+    )
+
+    # 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.utility.hub_utils import (
+        download_benchmark,
+        download_model,
+        download_pipeline,
+        query_models_info,
+    )
+    from omnigenbench.utility import hub_utils
+
+    # Import hub classes
+    from omnigenbench.utility.model_hub.model_hub import ModelHub
+    from omnigenbench.utility.dataset_hub.dataset_hub import load_benchmark_datasets
+    from omnigenbench.utility.pipeline_hub.pipeline import Pipeline
+    from omnigenbench.utility.pipeline_hub.pipeline_hub import PipelineHub
+
+    # Import module utilities
+    from omnigenbench.src.model.module_utils import OmniPooling
+    from omnigenbench.utility.ensemble import VoteEnsemblePredictor
+
+    # For backward compatibility version 0.2.7alpha and earlier
+    from omnigenbench.auto.config.auto_config import AutoBenchConfig
+
+    # 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__ = [
+        "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",
+        # 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",
+    ]
+
+except ImportError as e:
+    import warnings
+
+    warnings.warn(
+        f"Failed to import omnigenbench modules: {e}. "
+        "Please ensure omnigenbench is properly installed.\n"
+        "You can install it with: pip install omnigenbench\n"
+        "and replace all 'omnigenome' with 'omnigenbench' in your code.\n"
+        "e.g., from omnigenome import *  ->  from omnigenbench import *",
+        ImportWarning,
+    )
+
+    # Minimal fallback to prevent complete failure
+    __all__ = []

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/omnigenome.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.1a0
+Version: 0.3.3a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng
@@ -20,6 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: omnigenbench>=0.3.0
 Requires-Dist: findfile>=2.0.0
 Requires-Dist: autocuda>=0.16
 Requires-Dist: metric-visualizer>=0.9.6
@@ -34,7 +35,6 @@ Requires-Dist: transformers>=4.46.0
 Requires-Dist: packaging
 Requires-Dist: peft
 Requires-Dist: dill
-Requires-Dist: accelerate
 Provides-Extra: dev
 Requires-Dist: dill; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
@@ -54,7 +54,7 @@ Dynamic: summary
 
 ![favicon.png](asset/favicon.png)
 
-<h3 align="center">OmniGenBench is a modular benchmarking platform for evaluating genomic foundation models (GFMs) across diverse tasks like RNA structure prediction, gene function classification, and multi-species generalization.</h3>
+<h3 align="center">OmniGenBench offers an all-in-one solution for genomic foundation model finetuning, inference, deployment and automated benchmarking, designed for research and applications in genomics.</h3>
 
 <div align="center">
 
@@ -104,15 +104,15 @@ Dynamic: summary
 ## Installation
 
 ### Requirements
-Before installing OmniGenome, you need to install the following dependencies:
+Before installing OmniGenoBench, you need to install the following dependencies:
 - Python 3.10+
 - PyTorch 2.5+
 - Transformers 4.46.0+
 
 ### PyPI Installation
-To install OmniGenome, you can use pip:
+To install OmniGenoBench, you can use pip:
 ```bash
-pip install omnigenome -U
+pip install omnigenbench -U
 ```
 
 ### Source Installation
@@ -136,7 +136,7 @@ You can find a visualization of AutoBench [here](asset/AutoBench.gif).
 ### Auto-benchmark via Python API
 Or you can use the following python code to run the auto-benchmark:
 ```python
-from omnigenome import AutoBench
+from omnigenbench import AutoBench
 gfm = 'LongSafari/hyenadna-medium-160k-seqlen-hf'
 # benchmark could be "RGB", "GB", "PGB", "GUE", which will be downloaded from the Hugging Face model hub
 benchmark = "RGB"
@@ -185,7 +185,7 @@ OmniGenBench supports five curated benchmark suites covering both **sequence-lev
 ### RNA Design
 RNA design is a fundamental problem in synthetic biology,
 where the goal is to design RNA sequences that fold into a target structure.
-In this demo, we show how to use OmniGenome to design RNA sequences 
+In this demo, we show how to use OmniGenoBench to design RNA sequences 
 that fold into a target structure using a pre-trained model.
 The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_design/RNA_Design_Tutorial.ipynb).
 
@@ -195,7 +195,7 @@ You can find a visual example of RNA Design [here](asset/RNA_Design.gif).
 
 RNA secondary structure prediction is a fundamental problem in computational biology,
 where the goal is to predict the secondary structure of an RNA sequence.
-In this demo, we show how to use OmniGenome to predict the secondary structure of RNA sequences using a pre-trained model.
+In this demo, we show how to use OmniGenoBench to predict the secondary structure of RNA sequences using a pre-trained model.
 The tutorials of RNA Secondary Structure Prediction can be found in
 [Secondary_Structure_Prediction_Tutorial.ipynb](examples/rna_secondary_structure_prediction/Secondary_Structure_Prediction_Tutorial.ipynb).
 

omnigenome-0.3.3a0/omnigenome.egg-info/SOURCES.txt

@@ -0,0 +1,15 @@
+LICENSE
+setup.py
+setup_omnigenome.py
+omnigenome/__init__.py
+omnigenome.egg-info/PKG-INFO
+omnigenome.egg-info/SOURCES.txt
+omnigenome.egg-info/dependency_links.txt
+omnigenome.egg-info/entry_points.txt
+omnigenome.egg-info/requires.txt
+omnigenome.egg-info/top_level.txt
+tests/test_dataset_patterns.py
+tests/test_examples_syntax.py
+tests/test_model_loading.py
+tests/test_rna_functions.py
+tests/test_training_patterns.py

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/omnigenome.egg-info/requires.txt

@@ -1,3 +1,4 @@
+omnigenbench>=0.3.0
 findfile>=2.0.0
 autocuda>=0.16
 metric-visualizer>=0.9.6
@@ -12,7 +13,6 @@ transformers>=4.46.0
 packaging
 peft
 dill
-accelerate
 
 [dev]
 dill

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/setup.py

@@ -9,7 +9,7 @@
 
 from pathlib import Path
 from setuptools import setup, find_packages
-from omnigenome import __version__
+from omnigenbench import __version__
 
 cwd = Path(__file__).parent
 long_description = (cwd / "README.MD").read_text(encoding="utf8")
@@ -21,12 +21,12 @@ extras = {
     ]
 }
 
-# This is the main setup.py - it will build omnigenome by default
+# This is the main setup.py - it will build omnigenbench by default
 # Use setup_omnigenome.py and setup_omnigenbench.py for separate builds
 setup(
-    name="omnigenome",
+    name="omnigenbench",
     version=__version__,
-    description="OmniGenome: A comprehensive toolkit for genome analysis.",
+    description="OmniGenoBench: A comprehensive toolkit for genome analysis.",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/yangheng95/OmniGenBench",
@@ -37,11 +37,11 @@ setup(
     include_package_data=True,
     exclude_package_data={"": [".gitignore"]},
     license="Apache-2.0",
-    packages=find_packages(include=["omnigenome", "omnigenome.*"]),
+    packages=find_packages(include=["omnigenbench", "omnigenbench.*", "omnigenome", "omnigenome.*"]),
     entry_points={
         "console_scripts": [
-            "autobench=omnigenome:run_bench",
-            "autotrain=omnigenome:run_train",
+            "autobench=omnigenbench.auto.auto_bench.auto_bench_cli:run_bench",
+            "autotrain=omnigenbench.auto.auto_train.auto_train_cli:run_train",
         ],
     },
     install_requires=[

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/setup_omnigenome.py

@@ -9,6 +9,8 @@
 
 from pathlib import Path
 from setuptools import setup, find_packages
+
+# Define version directly to avoid circular import
 from omnigenome import __version__
 
 cwd = Path(__file__).parent
@@ -43,6 +45,7 @@ setup(
         ],
     },
     install_requires=[
+        "omnigenbench>=0.3.0",  # Add dependency on omnigenbench
         "findfile>=2.0.0",
         "autocuda>=0.16",
         "metric-visualizer>=0.9.6",
@@ -57,7 +60,6 @@ setup(
         "packaging",
         "peft",
         "dill",
-        "accelerate"
     ],
     extras_require=extras,
     classifiers=[

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/tests/test_dataset_patterns.py

@@ -14,11 +14,11 @@ class TestDatasetPatterns:
     def test_dataset_imports(self):
         """Test dataset class imports as shown in examples."""
         try:
-            from omnigenome import (
-                OmniGenomeDatasetForSequenceClassification,
-                OmniGenomeDatasetForSequenceRegression,
-                OmniGenomeDatasetForTokenClassification,
-                OmniGenomeDatasetForTokenRegression,
+            from omnigenbench import (
+                OmniDatasetForSequenceClassification,
+                OmniDatasetForSequenceRegression,
+                OmniDatasetForTokenClassification,
+                OmniDatasetForTokenRegression,
             )
             assert True
         except ImportError:
@@ -186,18 +186,18 @@ class TestDatasetPatterns:
     def test_dataset_initialization_pattern(self):
         """Test dataset initialization pattern from examples."""
         try:
-            from omnigenome import OmniGenomeDatasetForSequenceClassification
+            from omnigenbench import OmniDatasetForSequenceClassification
         except ImportError:
             pytest.skip("omnigenome not available")
             
-        with patch("omnigenome.OmniGenomeDatasetForSequenceClassification") as mock_dataset:
+        with patch("omnigenome.OmniDatasetForSequenceClassification") as mock_dataset:
             mock_dataset.return_value = MagicMock()
             
             # Create a single mock tokenizer instance to use in both call and assertion
             mock_tokenizer_instance = MagicMock()
             
             # Pattern from examples
-            dataset = OmniGenomeDatasetForSequenceClassification(
+            dataset = OmniDatasetForSequenceClassification(
                 train_file="path/to/train.json",
                 test_file="path/to/test.json",
                 tokenizer=mock_tokenizer_instance,

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/tests/test_model_loading.py

@@ -38,7 +38,7 @@ class TestModelLoading:
     def test_model_import_structure(self):
         """Test that model classes can be imported as shown in examples."""
         try:
-            from omnigenome import (
+            from omnigenbench import (
                 OmniModelForSequenceClassification,
                 OmniModelForTokenClassification,
                 OmniModelForSequenceRegression,
@@ -52,7 +52,7 @@ class TestModelLoading:
     def test_embedding_model_import(self):
         """Test embedding model import as shown in RNA_Embedding_Tutorial.ipynb."""
         try:
-            from omnigenome import OmniGenomeModelForEmbedding
+            from omnigenbench import OmniModelForEmbedding
             assert True
         except ImportError:
             pytest.skip("omnigenome not available or missing dependencies")
@@ -60,7 +60,7 @@ class TestModelLoading:
     def test_pooling_import(self):
         """Test pooling import as shown in classification.ipynb."""
         try:
-            from omnigenome import OmniModel, OmniPooling
+            from omnigenbench import OmniModel, OmniPooling
             assert True
         except ImportError:
             pytest.skip("omnigenome not available or missing dependencies")
@@ -94,17 +94,17 @@ class TestModelLoading:
             pytest.skip("torch not available")
             
         try:
-            from omnigenome import OmniGenomeModelForEmbedding
+            from omnigenbench import OmniModelForEmbedding
         except ImportError:
             pytest.skip("omnigenome not available")
             
-        with patch('omnigenome.OmniGenomeModelForEmbedding') as mock_embedding_model:
+        with patch('omnigenome.OmniModelForEmbedding') as mock_embedding_model:
             mock_instance = MagicMock()
             mock_instance.to.return_value = mock_instance
             mock_embedding_model.return_value = mock_instance
 
             model_name = "yangheng/OmniGenome-52M"
-            embedding_model = OmniGenomeModelForEmbedding(model_name, trust_remote_code=True).to(torch.device("cuda:0")).to(torch.float16)
+            embedding_model = OmniModelForEmbedding(model_name, trust_remote_code=True).to(torch.device("cuda:0")).to(torch.float16)
 
             # Verify initialization pattern
             mock_embedding_model.assert_called_once_with(model_name, trust_remote_code=True)
@@ -129,7 +129,7 @@ class TestModelLoading:
     def test_classification_model_initialization_pattern(self, mock_tokenizer):
         """Test classification model init pattern from examples."""
         try:
-            from omnigenome import OmniModelForSequenceClassification
+            from omnigenbench import OmniModelForSequenceClassification
         except ImportError:
             pytest.skip("omnigenome not available")
             

{omnigenome-0.3.1a0 → omnigenome-0.3.3a0}/tests/test_training_patterns.py

@@ -11,7 +11,7 @@ class TestTrainingPatterns:
     def test_trainer_imports(self):
         """Test trainer imports as shown in quick_start.md."""
         try:
-            from omnigenome import Trainer
+            from omnigenbench import Trainer
             assert True
         except ImportError:
             pytest.skip("omnigenome not available or missing dependencies")
@@ -19,7 +19,7 @@ class TestTrainingPatterns:
     def test_autobench_imports(self):
         """Test AutoBench imports from examples."""
         try:
-            from omnigenome import AutoBench
+            from omnigenbench import AutoBench
             assert True
         except ImportError:
             pytest.skip("omnigenome not available or missing dependencies")
@@ -42,7 +42,7 @@ class TestTrainingPatterns:
         mock_instance = MagicMock()
         mock_autobench.return_value = mock_instance
         
-        from omnigenome import AutoBench
+        from omnigenbench import AutoBench
         
         # Pattern from quick_start.md
         auto_bench = AutoBench(
@@ -83,7 +83,7 @@ class TestTrainingPatterns:
         """Test Trainer initialization pattern from quick_start.md."""
         mock_trainer.return_value = MagicMock()
         
-        from omnigenome import Trainer
+        from omnigenbench import Trainer
         
         # Mock training arguments
         mock_args = MagicMock()