omnigenome 0.3.13a0__py3-none-any.whl → 0.3.17a0__py3-none-any.whl

omnigenome/__init__.py

@@ -115,23 +115,23 @@ try:
     from omnigenbench.src.trainer.accelerate_trainer import AccelerateTrainer
 
     # Import hub utilities
-    from omnigenbench.utility.hub_utils import (
+    from omnigenbench.src.utility.hub_utils import (
         download_benchmark,
         download_model,
         download_pipeline,
         query_models_info,
     )
-    from omnigenbench.utility import hub_utils
+    from omnigenbench.src.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
+    from omnigenbench.src.utility.model_hub.model_hub import ModelHub
+    from omnigenbench.src.utility.dataset_hub import load_benchmark_datasets
+    from omnigenbench.src.utility.pipeline_hub 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.utility.ensemble import VoteEnsemblePredictor
+    from omnigenbench.src.utility import VoteEnsemblePredictor
 
     # For backward compatibility version 0.2.7alpha and earlier
     from omnigenbench.auto.config.auto_config import AutoBenchConfig

{omnigenome-0.3.13a0.dist-info → omnigenome-0.3.17a0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.13a0
+Version: 0.3.17a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng
@@ -145,7 +145,8 @@ seeds = [0, 1, 2, 3, 4]
 bench = AutoBench(benchmark=benchmark, model_name_or_path=gfm, overwrite=False)
 bench.run(autocast=False, batch_size=bench_size, seeds=seeds)
 ```
-You can find an example of AutoBench via Python API [here](examples/autobench/AutoBench_Tutorial.ipynb).
+You can find an example of AutoBench via Python API [here](examples/autobench_gfm_evaluation/benchmarking_with_lora.ipynb).
+
 
 ## Supported Models
 
@@ -187,9 +188,9 @@ 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 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).
+The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_sequence_design/RNA_Design_Tutorial.ipynb).
 
-You can find a visual example of RNA Design [here](asset/RNA_Design.gif).
+You can find a visual example of RNA Design [here](asset/RNADesign-Demo.gif).
 
 ### RNA Secondary Structure Prediction
 
@@ -199,10 +200,10 @@ In this demo, we show how to use OmniGenoBench to predict the secondary structur
 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).
 
-You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNA_Structure_Prediction.gif).
+You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNASSP-Demo.gif).
 
 ### More Tutorials
-Please find more usage tutorials in [examples/tutorials](examples/tutorials).
+Please find more usage tutorials in [examples](examples).
 
 ## Citation
 ```bibtex

omnigenome-0.3.17a0.dist-info/RECORD

@@ -0,0 +1,7 @@
+omnigenome/__init__.py,sha256=2JNoPrnv-1lYXkBiuHBYVXp1OJiRD8c9j65qFeXJtQY,9436
+omnigenome-0.3.17a0.dist-info/licenses/LICENSE,sha256=oQoefBV6siHctF0ET-OO3EaSZgtqGtf-wdIAmokS8iY,11560
+omnigenome-0.3.17a0.dist-info/METADATA,sha256=HpqOJcHgtAxMEpC9x8-21bQvAL5yfZ-7BNKmTRT23ow,10344
+omnigenome-0.3.17a0.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
+omnigenome-0.3.17a0.dist-info/entry_points.txt,sha256=uu40UgMPxY65ASdRbrhkwH94r7CIYgyG_iDBmqFQbD8,84
+omnigenome-0.3.17a0.dist-info/top_level.txt,sha256=LVFxm_WPaxjj9KnAqdW94W4D4lbOk30gdsaKlJiSzTo,11
+omnigenome-0.3.17a0.dist-info/RECORD,,

omnigenome-0.3.13a0.dist-info/RECORD

@@ -1,7 +0,0 @@
-omnigenome/__init__.py,sha256=Y3th9B_5xrJkzFXgR07FxSWP54NvuxD3XoJ17U5Db7s,9438
-omnigenome-0.3.13a0.dist-info/licenses/LICENSE,sha256=oQoefBV6siHctF0ET-OO3EaSZgtqGtf-wdIAmokS8iY,11560
-omnigenome-0.3.13a0.dist-info/METADATA,sha256=RZUK9vITBe9JlgliyCfzhfdyOvMch8gyJkWVFGljG6k,10343
-omnigenome-0.3.13a0.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
-omnigenome-0.3.13a0.dist-info/entry_points.txt,sha256=uu40UgMPxY65ASdRbrhkwH94r7CIYgyG_iDBmqFQbD8,84
-omnigenome-0.3.13a0.dist-info/top_level.txt,sha256=LVFxm_WPaxjj9KnAqdW94W4D4lbOk30gdsaKlJiSzTo,11
-omnigenome-0.3.13a0.dist-info/RECORD,,