test file removed

test_adapter_fix.py

@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-
-import sys
-import os
-from transformers import AutoModel, AutoTokenizer
-from transformers.utils import cached_file
-
-def test_adapter_from_outside():
-    """Test loading the adapter from outside the repository"""
-    print("🧪 Testing adapter loading from outside repository...")
-    
-    # Clear cache first
-    cache_dir = os.path.expanduser("~/.cache/huggingface/hub/models--hemantn--ablang2")
-    if os.path.exists(cache_dir):
-        import shutil
-        shutil.rmtree(cache_dir)
-        print("🗑️  Cleared Hugging Face cache")
-    
-    try:
-        # Load model and tokenizer
-        print("📥 Loading model and tokenizer...")
-        model = AutoModel.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-        tokenizer = AutoTokenizer.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-        
-        # Find the cached model directory and import adapter
-        adapter_path = cached_file("hemantn/ablang2", "adapter.py")
-        cached_model_dir = os.path.dirname(adapter_path)
-        sys.path.insert(0, cached_model_dir)
-        
-        print(f"📁 Cached model directory: {cached_model_dir}")
-        print(f"📄 Files in cached directory:")
-        for f in os.listdir(cached_model_dir):
-            print(f"   {f}")
-        
-        # Import and create the adapter
-        print("🔧 Importing adapter...")
-        from adapter import AbLang2PairedHuggingFaceAdapter
-        ablang = AbLang2PairedHuggingFaceAdapter(model=model, tokenizer=tokenizer)
-        print("✅ Adapter created successfully!")
-        
-        # Test basic functionality
-        print("🧬 Testing restore functionality...")
-        test_seq = [
-            'EVQ***SGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS',
-            'DIQLTQSPLSLPVTLGQPASISCRSS*SLEASDTNIYLSWFQQRPGQSPRRLIYKI*NRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK'
-        ]
-        
-        restored = ablang(test_seq, mode='restore')
-        print("✅ Restore functionality working!")
-        print(f"📊 Restored sequences: {len(restored)}")
-        
-        return True
-        
-    except Exception as e:
-        print(f"❌ Error: {e}")
-        import traceback
-        traceback.print_exc()
-        return False
-
-if __name__ == "__main__":
-    success = test_adapter_from_outside()
-    if success:
-        print("🎉 All tests passed! The adapter works from outside the repository.")
-    else:
-        print("💥 Tests failed. The adapter still has issues.") 

test_align.py

@@ -1,34 +0,0 @@
-import sys
-import os
-from transformers import AutoModel, AutoTokenizer
-from transformers.utils import cached_file
-
-# Load model and tokenizer from Hugging Face Hub
-print("Loading model and tokenizer...")
-model = AutoModel.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-tokenizer = AutoTokenizer.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-
-# Find the cached model directory and import adapter
-adapter_path = cached_file("hemantn/ablang2", "adapter.py")
-cached_model_dir = os.path.dirname(adapter_path)
-sys.path.insert(0, cached_model_dir)
-
-# Import and create the adapter
-from adapter import AbLang2PairedHuggingFaceAdapter
-ablang = AbLang2PairedHuggingFaceAdapter(model=model, tokenizer=tokenizer)
-
-# Test sequences from the notebook
-test_sequences = [
-    ['EVQ***SGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS',
-     'DIQLTQSPLSLPVTLGQPASISCRSS*SLEASDTNIYLSWFQQRPGQSPRRLIYKI*NRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK']
-]
-
-print("Testing restore without alignment:")
-result_no_align = ablang(test_sequences, mode='restore', align=False)
-print(f"Result (no align): {result_no_align[0]}")
-
-print("\nTesting restore with alignment:")
-result_with_align = ablang(test_sequences, mode='restore', align=True)
-print(f"Result (with align): {result_with_align[0]}")
-
-print("\nBoth options work correctly!") 

test_app_output.py

@@ -1,56 +0,0 @@
-import sys
-import os
-from transformers import AutoModel, AutoTokenizer
-from transformers.utils import cached_file
-
-# Load model and tokenizer from Hugging Face Hub
-print("Loading model and tokenizer...")
-model = AutoModel.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-tokenizer = AutoTokenizer.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-
-# Find the cached model directory and import adapter
-adapter_path = cached_file("hemantn/ablang2", "adapter.py")
-cached_model_dir = os.path.dirname(adapter_path)
-sys.path.insert(0, cached_model_dir)
-
-# Import and create the adapter
-from adapter import AbLang2PairedHuggingFaceAdapter
-ablang = AbLang2PairedHuggingFaceAdapter(model=model, tokenizer=tokenizer)
-
-def restore_sequences(heavy_chain, light_chain, use_align=False):
-    try:
-        # Prepare input sequences
-        if heavy_chain.strip() and light_chain.strip():
-            sequences = [[heavy_chain.strip(), light_chain.strip()]]
-        elif heavy_chain.strip():
-            sequences = [[heavy_chain.strip(), ""]]
-        elif light_chain.strip():
-            sequences = [["", light_chain.strip()]]
-        else:
-            return "Please provide at least one antibody chain sequence."
-        
-        # Perform restoration
-        restored = ablang(sequences, mode='restore', align=use_align)
-        
-        # Format output
-        if hasattr(restored, '__len__') and len(restored) > 0:
-            result = restored[0]  # Get the first (and only) result
-            return result
-        else:
-            return "Error: No restoration result obtained."
-            
-    except Exception as e:
-        return f"Error during restoration: {str(e)}"
-
-# Test the function
-heavy_chain = "EVQ***SGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS"
-light_chain = "DIQLTQSPLSLPVTLGQPASISCRSS*SLEASDTNIYLSWFQQRPGQSPRRLIYKI*NRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK"
-
-result = restore_sequences(heavy_chain, light_chain, False)
-print("="*80)
-print("APP OUTPUT TEST:")
-print("="*80)
-print(result)
-print("="*80)
-print(f"Result length: {len(result)}")
-print(f"Result type: {type(result)}") 

test_integrated_adapter.py

@@ -1,158 +0,0 @@
-#!/usr/bin/env python3
-"""
-Test script for the integrated AbLang2 adapter functionality.
-This script tests that all the utility files are properly integrated and the adapter works correctly.
-"""
-
-import sys
-import os
-
-# Global variable to store the adapter class
-AbLang2PairedHuggingFaceAdapter = None
-
-def test_imports():
-    """Test that all imports work correctly"""
-    global AbLang2PairedHuggingFaceAdapter
-    
-    print("🔍 Testing imports...")
-    
-    try:
-        # Test utility imports
-        from restoration import AbRestore
-        print("✅ AbRestore imported successfully")
-        
-        from ablang_encodings import AbEncoding
-        print("✅ AbEncoding imported successfully")
-        
-        from alignment import AbAlignment
-        print("✅ AbAlignment imported successfully")
-        
-        from scores import AbScores
-        print("✅ AbScores imported successfully")
-        
-        from extra_utils import res_to_seq, res_to_list
-        print("✅ extra_utils functions imported successfully")
-        
-        # Test adapter import
-        from adapter import AbLang2PairedHuggingFaceAdapter
-        print("✅ AbLang2PairedHuggingFaceAdapter imported successfully")
-        
-        print("\n🎉 All imports successful!")
-        return True
-        
-    except ImportError as e:
-        print(f"❌ Import error: {e}")
-        return False
-    except Exception as e:
-        print(f"❌ Unexpected error: {e}")
-        return False
-
-def test_model_loading():
-    """Test model loading from Hugging Face"""
-    global AbLang2PairedHuggingFaceAdapter
-    
-    print("\n🔍 Testing model loading...")
-    
-    try:
-        from transformers import AutoModel, AutoTokenizer
-        
-        print("Loading model from Hugging Face...")
-        model = AutoModel.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-        print("✅ Model loaded successfully")
-        
-        print("Loading tokenizer from Hugging Face...")
-        tokenizer = AutoTokenizer.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-        print("✅ Tokenizer loaded successfully")
-        
-        print("Creating adapter...")
-        ablang = AbLang2PairedHuggingFaceAdapter(model=model, tokenizer=tokenizer)
-        print("✅ Adapter created successfully")
-        
-        return True, ablang
-        
-    except ImportError as e:
-        print(f"❌ Transformers not available: {e}")
-        print("   This is expected if transformers is not installed")
-        return False, None
-    except Exception as e:
-        print(f"❌ Model loading error: {e}")
-        return False, None
-
-def test_restore_functionality(ablang):
-    """Test the restore functionality"""
-    print("\n🔍 Testing restore functionality...")
-    
-    try:
-        # Test sequences
-        test_sequences = [
-            ["EVQ***SGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS",
-             "DIQLTQSPLSLPVTLGQPASISCRSS*SLEASDTNIYLSWFQQRPGQSPRRLIYKI*NRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK"]
-        ]
-        
-        print("Testing restore without alignment...")
-        result = ablang(test_sequences, mode='restore', align=False)
-        print(f"✅ Restore result: {result}")
-        
-        print("Testing restore with alignment...")
-        result_align = ablang(test_sequences, mode='restore', align=True)
-        print(f"✅ Restore with alignment result: {result_align}")
-        
-        return True
-        
-    except Exception as e:
-        print(f"❌ Restore functionality error: {e}")
-        return False
-
-def test_encoding_functionality(ablang):
-    """Test the encoding functionality"""
-    print("\n🔍 Testing encoding functionality...")
-    
-    try:
-        test_sequences = [
-            ["EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMGWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDYPGHGAAFMDVWGQGTTVTVSS",
-             "DIQLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPTTFGQGTKVEIK"]
-        ]
-        
-        print("Testing sequence coding...")
-        result = ablang(test_sequences, mode='seqcoding')
-        print(f"✅ Sequence coding result shape: {result.shape if hasattr(result, 'shape') else len(result)}")
-        
-        return True
-        
-    except Exception as e:
-        print(f"❌ Encoding functionality error: {e}")
-        return False
-
-def main():
-    """Main test function"""
-    print("🧬 AbLang2 Integrated Adapter Test")
-    print("=" * 50)
-    
-    # Test imports
-    if not test_imports():
-        print("\n❌ Import tests failed. Exiting.")
-        return
-    
-    # Test model loading
-    model_loaded, ablang = test_model_loading()
-    
-    if model_loaded and ablang is not None:
-        # Test functionality
-        test_restore_functionality(ablang)
-        test_encoding_functionality(ablang)
-        
-        print("\n🎉 All tests completed successfully!")
-        print("\n📋 Summary:")
-        print("✅ All utility files integrated")
-        print("✅ Adapter imports working")
-        print("✅ Model loading successful")
-        print("✅ Restore functionality working")
-        print("✅ Encoding functionality working")
-        
-    else:
-        print("\n⚠️  Model loading test skipped (transformers not available)")
-        print("✅ Core integration tests passed")
-        print("✅ Ready for deployment")
-
-if __name__ == "__main__":
-    main() 

test_module_loading.py

@@ -1,19 +0,0 @@
-import sys
-import os
-import numpy as np
-from transformers import AutoModel, AutoTokenizer
-from transformers.utils import cached_file
-
-# Load model and tokenizer from Hugging Face Hub
-model = AutoModel.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-tokenizer = AutoTokenizer.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-
-# Find the cached model directory and import adapter
-adapter_path = cached_file("hemantn/ablang2", "adapter.py")
-cached_model_dir = os.path.dirname(adapter_path)
-sys.path.insert(0, cached_model_dir)
-
-# Import and create the adapter
-from adapter import AbLang2PairedHuggingFaceAdapter
-ablang = AbLang2PairedHuggingFaceAdapter(model=model, tokenizer=tokenizer)
-

test_original_compatibility.py

@@ -1,69 +0,0 @@
-#!/usr/bin/env python3
-
-import sys
-import os
-from transformers import AutoModel, AutoTokenizer
-from transformers.utils import cached_file
-
-def test_original_compatibility():
-    """Test that our adapter produces the same results as the original"""
-    print("🧪 Testing compatibility with original AbLang2_final_version...")
-    
-    try:
-        # Load model and tokenizer
-        print("📥 Loading model and tokenizer...")
-        model = AutoModel.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-        tokenizer = AutoTokenizer.from_pretrained("hemantn/ablang2", trust_remote_code=True)
-        
-        # Find the cached model directory and import adapter
-        adapter_path = cached_file("hemantn/ablang2", "adapter.py")
-        cached_model_dir = os.path.dirname(adapter_path)
-        sys.path.insert(0, cached_model_dir)
-        
-        # Import and create the adapter
-        print("🔧 Importing adapter...")
-        from adapter import AbLang2PairedHuggingFaceAdapter
-        ablang = AbLang2PairedHuggingFaceAdapter(model=model, tokenizer=tokenizer)
-        print("✅ Adapter created successfully!")
-        
-        # Test with the same sequences as in the notebook
-        print("🧬 Testing with notebook sequences...")
-        test_seqs = [
-            ['EVQ***SGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS', 'DIQLTQSPLSLPVTLGQPASISCRSS*SLEASDTNIYLSWFQQRPGQSPRRLIYKI*NRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK'],
-            ['EVQLLESGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS', 'DIQLTQSPLSLPVTLGQPASISCRSSQSLEASDTNIYLSWFQQRPGQSPRRLIYKISNRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK']
-        ]
-        
-        # Test restore functionality
-        print("🔧 Testing restore functionality...")
-        restored = ablang(test_seqs, mode='restore')
-        print("✅ Restore functionality working!")
-        print(f"📊 Restored sequences: {len(restored)}")
-        for i, seq in enumerate(restored):
-            print(f"   Sequence {i+1}: {seq[:50]}...")
-        
-        # Test seqcoding functionality
-        print("🔧 Testing seqcoding functionality...")
-        seqcodings = ablang(test_seqs, mode='seqcoding')
-        print("✅ Seqcoding functionality working!")
-        print(f"📊 Seqcoding shape: {seqcodings.shape}")
-        
-        # Test confidence functionality
-        print("🔧 Testing confidence functionality...")
-        confidence_scores = ablang(test_seqs, mode='confidence')
-        print("✅ Confidence functionality working!")
-        print(f"📊 Confidence scores: {confidence_scores}")
-        
-        return True
-        
-    except Exception as e:
-        print(f"❌ Error: {e}")
-        import traceback
-        traceback.print_exc()
-        return False
-
-if __name__ == "__main__":
-    success = test_original_compatibility()
-    if success:
-        print("🎉 All tests passed! The adapter is compatible with the original.")
-    else:
-        print("💥 Tests failed. There are compatibility issues.")