omnigenome 0.3.25a0__tar.gz → 0.3.27a0__tar.gz

{omnigenome-0.3.25a0 → omnigenome-0.3.27a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.25a0
+Version: 0.3.27a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng
@@ -182,7 +182,7 @@ ogb autobench \
     --trainer accelerate
 
 # Legacy command (still supported for backward compatibility)
-# autobench --model_name_or_path "yangheng/OmniGenome-186M" --benchmark "RGB"
+# autobench --config_or_model "yangheng/OmniGenome-186M" --benchmark "RGB"
 ```
 **Output**: Results include mean ± standard deviation for each metric (e.g., MCC: 0.742 ± 0.015, F1: 0.863 ± 0.009)
 
@@ -202,7 +202,7 @@ seeds = [0, 1, 2, 3, 4]  # Multi-seed for statistical rigor
 # Run automated evaluation
 bench = AutoBench(
     benchmark=benchmark,
-    model_name_or_path=gfm,
+    config_or_model=gfm,
     overwrite=False  # Skip completed tasks
 )
 bench.run(autocast=False, batch_size=bench_size, seeds=seeds)

{omnigenome-0.3.25a0 → omnigenome-0.3.27a0}/omnigenome.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.25a0
+Version: 0.3.27a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng
@@ -182,7 +182,7 @@ ogb autobench \
     --trainer accelerate
 
 # Legacy command (still supported for backward compatibility)
-# autobench --model_name_or_path "yangheng/OmniGenome-186M" --benchmark "RGB"
+# autobench --config_or_model "yangheng/OmniGenome-186M" --benchmark "RGB"
 ```
 **Output**: Results include mean ± standard deviation for each metric (e.g., MCC: 0.742 ± 0.015, F1: 0.863 ± 0.009)
 
@@ -202,7 +202,7 @@ seeds = [0, 1, 2, 3, 4]  # Multi-seed for statistical rigor
 # Run automated evaluation
 bench = AutoBench(
     benchmark=benchmark,
-    model_name_or_path=gfm,
+    config_or_model=gfm,
     overwrite=False  # Skip completed tasks
 )
 bench.run(autocast=False, batch_size=bench_size, seeds=seeds)

{omnigenome-0.3.25a0 → omnigenome-0.3.27a0}/tests/test_attention_extraction.py

@@ -46,7 +46,7 @@ class TestAttentionExtractionEmbeddingModel:
     @pytest.fixture(scope="class")
     def embedding_model(self, model_name):
         """Load embedding model for attention extraction"""
-        # OmniModelForEmbedding takes model_name_or_path as first positional argument
+        # OmniModelForEmbedding takes config_or_model as first positional argument
         model = OmniModelForEmbedding(model_name, trust_remote_code=True)
         return model
 

{omnigenome-0.3.25a0 → omnigenome-0.3.27a0}/tests/test_autobench_autotrain.py

@@ -60,7 +60,7 @@ class TestAutoBenchAPI:
         # Basic initialization
         bench = AutoBench(
             benchmark="RGB",
-            model_name_or_path="yangheng/OmniGenome-186M",
+            config_or_model="yangheng/OmniGenome-186M",
             overwrite=False
         )
         
@@ -72,7 +72,7 @@ class TestAutoBenchAPI:
         for benchmark in benchmark_names:
             bench = AutoBench(
                 benchmark=benchmark,
-                model_name_or_path="yangheng/OmniGenome-186M",
+                config_or_model="yangheng/OmniGenome-186M",
             )
             assert bench is not None
     
@@ -80,7 +80,7 @@ class TestAutoBenchAPI:
         """Test AutoBench accepts various configuration options"""
         bench = AutoBench(
             benchmark="RGB",
-            model_name_or_path="yangheng/OmniGenome-186M",
+            config_or_model="yangheng/OmniGenome-186M",
             tokenizer_name_or_path="yangheng/OmniGenome-186M",
             trainer="accelerate",
             overwrite=True,
@@ -98,7 +98,7 @@ class TestAutoBenchAPI:
         # Use smallest model and single seed for speed
         bench = AutoBench(
             benchmark="RGB",
-            model_name_or_path="yangheng/OmniGenome-52M",
+            config_or_model="yangheng/OmniGenome-52M",
             overwrite=True,
         )
         
@@ -121,7 +121,7 @@ class TestAutoBenchAPI:
         """Test AutoBench supports multi-seed evaluation"""
         bench = AutoBench(
             benchmark="RGB",
-            model_name_or_path="yangheng/OmniGenome-186M",
+            config_or_model="yangheng/OmniGenome-186M",
         )
         
         # Configuration with multiple seeds (as in examples)
@@ -147,7 +147,7 @@ class TestAutoTrainAPI:
         """Test AutoTrain can be initialized"""
         trainer = AutoTrain(
             dataset_name_or_path="translation_efficiency_prediction",
-            model_name_or_path="yangheng/PlantRNA-FM",
+            config_or_model="yangheng/PlantRNA-FM",
         )
         
         assert trainer is not None
@@ -159,7 +159,7 @@ class TestAutoTrainAPI:
         
         trainer = AutoTrain(
             dataset_name_or_path="translation_efficiency_prediction",
-            model_name_or_path="yangheng/PlantRNA-FM",
+            config_or_model="yangheng/PlantRNA-FM",
             output_dir=str(output_dir),
             num_labels=2,
             max_length=512,
@@ -188,7 +188,7 @@ class TestAutoTrainAPI:
         for config in task_configs:
             trainer = AutoTrain(
                 dataset_name_or_path=config["dataset"],
-                model_name_or_path="yangheng/OmniGenome-52M",
+                config_or_model="yangheng/OmniGenome-52M",
                 num_labels=config["num_labels"],
             )
             assert trainer is not None
@@ -204,7 +204,7 @@ class TestAutoTrainAPI:
         
         trainer = AutoTrain(
             dataset_name_or_path="translation_efficiency_prediction",
-            model_name_or_path="yangheng/PlantRNA-FM",
+            config_or_model="yangheng/PlantRNA-FM",
             output_dir=str(output_dir),
             epochs=1,
             batch_size=4,
@@ -387,7 +387,7 @@ class TestAutoWorkflowIntegration:
         # Step 1: Train a custom model
         trainer = AutoTrain(
             dataset_name_or_path="translation_efficiency_prediction",
-            model_name_or_path="yangheng/PlantRNA-FM",
+            config_or_model="yangheng/PlantRNA-FM",
             output_dir=str(output_dir),
             epochs=1,
             batch_size=4,
@@ -396,7 +396,7 @@ class TestAutoWorkflowIntegration:
         # Step 2: Benchmark the trained model
         bench = AutoBench(
             benchmark="RGB",
-            model_name_or_path=str(output_dir),
+            config_or_model=str(output_dir),
             overwrite=True,
         )
         
@@ -420,7 +420,7 @@ class TestAutoWorkflowIntegration:
         for model in models:
             bench = AutoBench(
                 benchmark=benchmark,
-                model_name_or_path=model,
+                config_or_model=model,
             )
             benches.append(bench)
         
@@ -448,7 +448,7 @@ class TestRealWorldBenchmarks:
         
         bench = AutoBench(
             benchmark="RGB",
-            model_name_or_path="yangheng/OmniGenome-52M",
+            config_or_model="yangheng/OmniGenome-52M",
             overwrite=True,
         )