omnigenome 0.3.26a0__tar.gz → 0.3.27a0__tar.gz

{omnigenome-0.3.26a0 → omnigenome-0.3.27a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.26a0
+Version: 0.3.27a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng

{omnigenome-0.3.26a0 → omnigenome-0.3.27a0}/omnigenome.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: omnigenome
-Version: 0.3.26a0
+Version: 0.3.27a0
 Summary: OmniGenome: A comprehensive toolkit for genome analysis.
 Home-page: https://github.com/yangheng95/OmniGenBench
 Author: Yang, Heng

{omnigenome-0.3.26a0 → omnigenome-0.3.27a0}/omnigenome.egg-info/SOURCES.txt

@@ -11,7 +11,6 @@ omnigenome.egg-info/top_level.txt
 tests/test_attention_extraction.py
 tests/test_autobench_autotrain.py
 tests/test_autoinfer_cli.py
-tests/test_benchmark_download.py
 tests/test_cli_commands.py
 tests/test_genomic_embeddings.py
 tests/test_hf_download.py

omnigenome-0.3.26a0/tests/test_benchmark_download.py

@@ -1,331 +0,0 @@
-# -*- coding: utf-8 -*-
-# file: test_benchmark_download.py
-# time: 18:30 01/11/2025
-# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
-# github: https://github.com/yangheng95
-# Copyright (C) 2019-2025. All Rights Reserved.
-
-"""
-Tests for robust benchmark and dataset downloading functionality.
-
-This module tests the enhanced download infrastructure that eliminates Git-LFS
-dependencies and provides automatic integrity verification.
-"""
-
-import os
-import shutil
-import pytest
-from pathlib import Path
-
-from omnigenbench.src.utility.hub_utils import download_benchmark
-from omnigenbench.src.utility.model_hub.hf_download import (
-    download_from_hf_hub,
-    verify_download_integrity,
-    list_hf_repo_files,
-    get_model_info,
-)
-
-
-class TestBenchmarkDownload:
-    """Test suite for benchmark downloading with HuggingFace Hub API."""
-
-    @pytest.fixture
-    def test_cache_dir(self, tmp_path):
-        """Create temporary cache directory for tests."""
-        cache_dir = tmp_path / "test_benchmarks"
-        cache_dir.mkdir(exist_ok=True)
-        yield str(cache_dir)
-        # Cleanup after test
-        if cache_dir.exists():
-            shutil.rmtree(cache_dir)
-
-    def test_download_benchmark_by_name(self, test_cache_dir):
-        """
-        Test downloading benchmark by short name with HF Hub API.
-        
-        Expected: Benchmark should be downloaded to cache directory.
-        """
-        try:
-            benchmark_path = download_benchmark(
-                "RGB",
-                use_hf_api=True,
-                cache_dir=test_cache_dir,
-                force_download=False,
-            )
-            
-            # Verify path exists
-            assert os.path.exists(benchmark_path), f"Benchmark path does not exist: {benchmark_path}"
-            
-            # Verify it's a directory
-            assert os.path.isdir(benchmark_path), f"Benchmark path is not a directory: {benchmark_path}"
-            
-            print(f"[SUCCESS] Benchmark downloaded to: {benchmark_path}")
-            
-        except Exception as e:
-            # If HF Hub doesn't have this benchmark, test passes with warning
-            pytest.skip(f"Benchmark not available on HF Hub: {e}")
-
-    def test_download_benchmark_from_hf_repo(self, test_cache_dir):
-        """
-        Test downloading benchmark from HuggingFace dataset repository.
-        
-        Expected: Benchmark should be downloaded using HF dataset identifier.
-        """
-        try:
-            benchmark_path = download_benchmark(
-                "yangheng/OmniGenBench_RGB",
-                use_hf_api=True,
-                cache_dir=test_cache_dir,
-            )
-            
-            assert os.path.exists(benchmark_path)
-            assert os.path.isdir(benchmark_path)
-            
-            print(f"[SUCCESS] Benchmark from HF repo: {benchmark_path}")
-            
-        except Exception as e:
-            pytest.skip(f"HF dataset not available: {e}")
-
-    def test_download_benchmark_force_redownload(self, test_cache_dir):
-        """
-        Test force re-downloading benchmark to update cache.
-        
-        Expected: Benchmark should be re-downloaded even if cached.
-        """
-        try:
-            # First download
-            benchmark_path1 = download_benchmark(
-                "RGB",
-                use_hf_api=True,
-                cache_dir=test_cache_dir,
-                force_download=False,
-            )
-            
-            # Force re-download
-            benchmark_path2 = download_benchmark(
-                "RGB",
-                use_hf_api=True,
-                cache_dir=test_cache_dir,
-                force_download=True,
-            )
-            
-            # Both should point to same location
-            assert benchmark_path1 == benchmark_path2
-            assert os.path.exists(benchmark_path2)
-            
-            print(f"[SUCCESS] Force re-download completed: {benchmark_path2}")
-            
-        except Exception as e:
-            pytest.skip(f"Force re-download test skipped: {e}")
-
-    def test_download_benchmark_fallback(self, test_cache_dir):
-        """
-        Test fallback to legacy HTTP download when HF Hub is unavailable.
-        
-        Expected: Should fall back to OmniGenome Space repository.
-        """
-        try:
-            # Try with use_hf_api=False to test fallback
-            benchmark_path = download_benchmark(
-                "RGB",
-                use_hf_api=False,  # Force legacy method
-                cache_dir=test_cache_dir,
-            )
-            
-            assert os.path.exists(benchmark_path)
-            assert os.path.isdir(benchmark_path)
-            
-            print(f"[SUCCESS] Fallback download completed: {benchmark_path}")
-            
-        except Exception as e:
-            pytest.skip(f"Fallback download test: {e}")
-
-
-class TestDatasetDownload:
-    """Test suite for dataset downloading via HuggingFace Hub API."""
-
-    @pytest.fixture
-    def test_cache_dir(self, tmp_path):
-        """Create temporary cache directory for tests."""
-        cache_dir = tmp_path / "test_datasets"
-        cache_dir.mkdir(exist_ok=True)
-        yield str(cache_dir)
-        if cache_dir.exists():
-            shutil.rmtree(cache_dir)
-
-    def test_download_dataset_from_hf_hub(self, test_cache_dir):
-        """
-        Test downloading dataset from HuggingFace Hub.
-        
-        Expected: Dataset should be downloaded successfully.
-        """
-        try:
-            dataset_path = download_from_hf_hub(
-                repo_id="yangheng/test_genomic_dataset",
-                repo_type="dataset",
-                cache_dir=test_cache_dir,
-                force_download=False,
-            )
-            
-            assert os.path.exists(dataset_path)
-            
-            # Verify integrity
-            is_valid = verify_download_integrity(dataset_path)
-            print(f"[INFO] Dataset integrity: {'Valid' if is_valid else 'Corrupted'}")
-            
-            print(f"[SUCCESS] Dataset downloaded to: {dataset_path}")
-            
-        except Exception as e:
-            pytest.skip(f"Dataset download test: {e}")
-
-    def test_selective_dataset_download(self, test_cache_dir):
-        """
-        Test selective file download for bandwidth optimization.
-        
-        Expected: Only specified file patterns should be downloaded.
-        """
-        try:
-            dataset_path = download_from_hf_hub(
-                repo_id="yangheng/test_genomic_dataset",
-                repo_type="dataset",
-                cache_dir=test_cache_dir,
-                allow_patterns=["*.json", "*.txt"],
-                ignore_patterns=["*.zip", "*.tar.gz"],
-            )
-            
-            assert os.path.exists(dataset_path)
-            
-            # Check that only allowed patterns exist
-            files = list(Path(dataset_path).rglob("*"))
-            json_txt_files = [f for f in files if f.suffix in [".json", ".txt"]]
-            zip_files = [f for f in files if f.suffix in [".zip", ".tar.gz"]]
-            
-            assert len(zip_files) == 0, "Ignored patterns should not be downloaded"
-            
-            print(f"[SUCCESS] Selective download: {len(json_txt_files)} files")
-            
-        except Exception as e:
-            pytest.skip(f"Selective download test: {e}")
-
-
-class TestMetadataQuery:
-    """Test suite for querying benchmark/dataset metadata."""
-
-    def test_list_repo_files(self):
-        """
-        Test listing files in a HuggingFace repository.
-        
-        Expected: Should return list of file paths.
-        """
-        try:
-            files = list_hf_repo_files(
-                "yangheng/OmniGenome-186M",
-                repo_type="model"
-            )
-            
-            assert isinstance(files, list), "Should return list of files"
-            assert len(files) > 0, "Should have at least some files"
-            
-            # Check for common model files
-            file_names = [os.path.basename(f) for f in files]
-            assert "config.json" in file_names, "Should have config.json"
-            
-            print(f"[SUCCESS] Found {len(files)} files in repository")
-            
-        except Exception as e:
-            pytest.skip(f"File listing test: {e}")
-
-    def test_get_model_info(self):
-        """
-        Test retrieving model repository metadata.
-        
-        Expected: Should return dict with metadata.
-        """
-        try:
-            info = get_model_info("yangheng/OmniGenome-186M")
-            
-            assert isinstance(info, dict), "Should return dictionary"
-            assert "id" in info or "modelId" in info, "Should have ID field"
-            
-            # Check for siblings (files)
-            if "siblings" in info:
-                total_size = sum(f.get("size", 0) for f in info["siblings"])
-                print(f"[INFO] Total model size: {total_size / (1024**2):.1f} MB")
-            
-            print(f"[SUCCESS] Retrieved metadata for model")
-            
-        except Exception as e:
-            pytest.skip(f"Metadata query test: {e}")
-
-
-class TestIntegrationWithAutoBench:
-    """Test integration of robust downloading with AutoBench."""
-
-    def test_autobench_automatic_download(self):
-        """
-        Test that AutoBench automatically uses robust downloading.
-        
-        Expected: Benchmark should be downloaded automatically when AutoBench is initialized.
-        """
-        try:
-            from omnigenbench import AutoBench
-            
-            # Initialize AutoBench - should automatically download benchmark
-            bench = AutoBench(
-                benchmark="RGB",
-                config_or_model="yangheng/OmniGenome-186M",
-                trainer="native",
-            )
-            
-            # Check that benchmark was downloaded
-            assert os.path.exists(bench.benchmark), f"Benchmark not downloaded: {bench.benchmark}"
-            assert os.path.isdir(bench.benchmark), "Benchmark should be a directory"
-            
-            # Check for metadata file
-            metadata_path = os.path.join(bench.benchmark, "metadata.py")
-            assert os.path.exists(metadata_path), "Benchmark should have metadata.py"
-            
-            print(f"[SUCCESS] AutoBench initialized with benchmark at: {bench.benchmark}")
-            
-        except Exception as e:
-            pytest.skip(f"AutoBench integration test: {e}")
-
-
-# Utility tests
-def test_benchmark_download_without_hf_api():
-    """
-    Test benchmark download with HF Hub API disabled (legacy method).
-    
-    Expected: Should use legacy HTTP download from OmniGenome Space.
-    """
-    try:
-        benchmark_path = download_benchmark(
-            "RGB",
-            use_hf_api=False,  # Disable HF Hub API
-        )
-        
-        assert os.path.exists(benchmark_path)
-        print(f"[SUCCESS] Legacy download method works: {benchmark_path}")
-        
-    except Exception as e:
-        pytest.skip(f"Legacy download test: {e}")
-
-
-def test_benchmark_download_with_invalid_name():
-    """
-    Test error handling for invalid benchmark names.
-    
-    Expected: Should raise ValueError or skip gracefully.
-    """
-    with pytest.raises((ValueError, Exception)):
-        download_benchmark(
-            "NonExistentBenchmark123456",
-            use_hf_api=True,
-        )
-    
-    print("[SUCCESS] Invalid benchmark name handled correctly")
-
-
-if __name__ == "__main__":
-    # Run tests with pytest
-    pytest.main([__file__, "-v", "-s"])