Coverage for ezstitcher/core/main.py: 0%

1""" 

2Main module for ezstitcher. 

3 

4This module provides the main entry point for the ezstitcher package. 

5""" 

6 

7import logging 

8from pathlib import Path 

9 

10# Import configuration classes 

11from ezstitcher.core.config import PipelineConfig 

12 

13# Import the pipeline orchestrator 

14from ezstitcher.core.pipeline_orchestrator import PipelineOrchestrator 

15 

16def apply_nested_overrides(config_obj, overrides): 

17 """ 

18 Recursively apply overrides to a nested config object. 

19 

20 Args: 

21 config_obj: The root config object. 

22 overrides: Dict of overrides, possibly with dot notation keys. 

23 """ 

24 for key, value in overrides.items(): 

25 parts = key.split(".") 

26 target = config_obj 

27 for part in parts[:-1]: 

28 if hasattr(target, part): 

29 target = getattr(target, part) 

30 else: 

31 # Invalid path, skip 

32 target = None 

33 break 

34 if target is not None and hasattr(target, parts[-1]): 

35 setattr(target, parts[-1], value) 

36 

37 

38 

39def process_plate( 

40 plate_folder: str | Path, 

41 config = None, 

42 **kwargs 

43) -> bool: 

44 """ 

45 High-level function to process a plate folder using the PipelineOrchestrator. 

46 

47 Args: 

48 plate_folder: Path to the plate folder. 

49 config: Optional PipelineConfig. If None, a default config is created. 

50 **kwargs: Optional overrides for config parameters. 

51 

52 Returns: 

53 True if processing succeeded, False otherwise. 

54 """ 

55 plate_folder = Path(plate_folder) 

56 

57 # Create default config if none provided 

58 if config is None: 

59 config = PipelineConfig() 

60 logging.info("No config provided, using default pipeline configuration") 

61 

62 # Apply any config overrides in kwargs 

63 apply_nested_overrides(config, kwargs) 

64 

65 # Create and run the pipeline 

66 pipeline = PipelineOrchestrator(config) 

67 return pipeline.run(plate_folder)