omnigenome 0.3.12a0__py3-none-any.whl → 0.3.15a0__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-0.3.12a0.dist-info → omnigenome-0.3.15a0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.1
 Name: omnigenome
-Version: 0.3.12a0
+Version: 0.3.15a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng
@@ -20,37 +20,24 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: omnigenbench>=0.3.3
-Requires-Dist: findfile>=2.0.0
-Requires-Dist: autocuda>=0.16
-Requires-Dist: metric-visualizer>=0.9.6
+Requires-Dist: omnigenbench >=0.3.3
+Requires-Dist: findfile >=2.0.0
+Requires-Dist: autocuda >=0.16
+Requires-Dist: metric-visualizer >=0.9.6
 Requires-Dist: termcolor
 Requires-Dist: gitpython
-Requires-Dist: torch>=2.6.0
+Requires-Dist: torch >=2.6.0
 Requires-Dist: pandas
 Requires-Dist: viennarna
 Requires-Dist: scikit-learn
 Requires-Dist: accelerate
-Requires-Dist: transformers>=4.46.0
+Requires-Dist: transformers >=4.46.0
 Requires-Dist: packaging
 Requires-Dist: peft
 Requires-Dist: dill
 Provides-Extra: dev
-Requires-Dist: dill; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
-Dynamic: license-file
-Dynamic: platform
-Dynamic: provides-extra
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
+Requires-Dist: dill ; extra == 'dev'
+Requires-Dist: pytest ; extra == 'dev'
 
 ![favicon.png](asset/favicon.png)
 
@@ -145,7 +132,8 @@ 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 +175,9 @@ 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 +187,10 @@ 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-0.3.15a0.dist-info/RECORD

@@ -0,0 +1,7 @@
+omnigenome/__init__.py,sha256=2JNoPrnv-1lYXkBiuHBYVXp1OJiRD8c9j65qFeXJtQY,9436
+omnigenome-0.3.15a0.dist-info/LICENSE,sha256=oQoefBV6siHctF0ET-OO3EaSZgtqGtf-wdIAmokS8iY,11560
+omnigenome-0.3.15a0.dist-info/METADATA,sha256=Uu-dZtcV_-RM7pk6SfU6ZgXb0bNvyvWkfxYMyNPm6XI,10061
+omnigenome-0.3.15a0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+omnigenome-0.3.15a0.dist-info/entry_points.txt,sha256=uu40UgMPxY65ASdRbrhkwH94r7CIYgyG_iDBmqFQbD8,84
+omnigenome-0.3.15a0.dist-info/top_level.txt,sha256=LVFxm_WPaxjj9KnAqdW94W4D4lbOk30gdsaKlJiSzTo,11
+omnigenome-0.3.15a0.dist-info/RECORD,,

{omnigenome-0.3.12a0.dist-info → omnigenome-0.3.15a0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (79.0.1)
+Generator: bdist_wheel (0.41.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

omnigenome-0.3.12a0.dist-info/RECORD

@@ -1,7 +0,0 @@
-omnigenome/__init__.py,sha256=Y3th9B_5xrJkzFXgR07FxSWP54NvuxD3XoJ17U5Db7s,9438
-omnigenome-0.3.12a0.dist-info/licenses/LICENSE,sha256=oQoefBV6siHctF0ET-OO3EaSZgtqGtf-wdIAmokS8iY,11560
-omnigenome-0.3.12a0.dist-info/METADATA,sha256=nFEj1k_wCBThaOpjl43RxxPTsiCuQSqMaWhrgR-to6Y,10343
-omnigenome-0.3.12a0.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
-omnigenome-0.3.12a0.dist-info/entry_points.txt,sha256=uu40UgMPxY65ASdRbrhkwH94r7CIYgyG_iDBmqFQbD8,84
-omnigenome-0.3.12a0.dist-info/top_level.txt,sha256=LVFxm_WPaxjj9KnAqdW94W4D4lbOk30gdsaKlJiSzTo,11
-omnigenome-0.3.12a0.dist-info/RECORD,,