masster 0.5.22__py3-none-any.whl → 0.5.24__py3-none-any.whl

masster/wizard/wizard.py

@@ -34,6 +34,7 @@ wizard = Wizard(
 
 from __future__ import annotations
 
+from math import e
 import os
 import sys
 import time
@@ -58,99 +59,99 @@ from masster._version import __version__ as version
 class wizard_def:
     """
     Default parameters for the Wizard automated processing system.
-    
+
     This class provides comprehensive configuration for all stages of automated
     mass spectrometry data processing from raw files to final results.
-    
+
     Attributes:
         # Core Configuration
         source (str): Path to directory containing raw data files
         folder (str): Output directory for processed study
         polarity (Optional[str]): Ion polarity mode ("positive", "negative", or None for auto-detection)
         num_cores (int): Number of CPU cores to use for parallel processing
-        
+
         # File Discovery
         file_extensions (List[str]): File extensions to search for
         search_subfolders (bool): Whether to search subdirectories
         skip_patterns (List[str]): Filename patterns to skip
-        
+
         # Processing Parameters
         adducts (List[str]): Adduct specifications for given polarity
         batch_size (int): Number of files to process per batch
         memory_limit_gb (float): Memory limit for processing (GB)
-        
+
         # Resume & Recovery
         resume_enabled (bool): Enable automatic resume capability
         force_reprocess (bool): Force reprocessing of existing files
         backup_enabled (bool): Create backups of intermediate results
-        
+
         # Output & Export
         generate_plots (bool): Generate visualization plots
         export_formats (List[str]): Output formats to generate
         compress_output (bool): Compress final study file
-        
+
         # Logging
         log_level (str): Logging detail level
         log_to_file (bool): Save logs to file
         progress_interval (int): Progress update interval (seconds)
     """
-    
+
     # === Core Configuration ===
     source: str = ""
-    folder: str = ""  
+    folder: str = ""
     polarity: Optional[str] = None
     num_cores: int = 4
-    
+
     # === File Discovery ===
     file_extensions: List[str] = field(default_factory=lambda: [".wiff", ".raw", ".mzML"])
     search_subfolders: bool = True
     skip_patterns: List[str] = field(default_factory=lambda: ["blank", "test"])
-    
+
     # === Processing Parameters ===
     adducts: List[str] = field(default_factory=list)  # Will be set based on polarity
     batch_size: int = 8
     memory_limit_gb: float = 16.0
     max_file_size_gb: float = 4.0
-    
+
     # === Resume & Recovery ===
     resume_enabled: bool = True
     force_reprocess: bool = False
     backup_enabled: bool = True
     checkpoint_interval: int = 10  # Save progress every N files
-    
+
     # === Study Assembly ===
     min_samples_for_merge: int = 2
     rt_tolerance: float = 1.5
     mz_max_diff: float = 0.01
     alignment_algorithm: str = "kd"
     merge_method: str = "qt"
-    
+
     # === Feature Detection ===
-    chrom_fwhm: float = 0.5
-    noise: float = 50.0
+    chrom_fwhm: float | None = None
+    noise: float | None = None
     chrom_peak_snr: float = 5.0
     tol_ppm: float = 10.0
     detector_type: str = "unknown"  # Detected detector type ("orbitrap", "quadrupole", "unknown")
-    
+
     # === Output & Export ===
     generate_plots: bool = True
     generate_interactive: bool = True
     export_formats: List[str] = field(default_factory=lambda: ["csv", "mgf", "xlsx"])
     compress_output: bool = True
     adaptive_compression: bool = True  # Adapt based on study size
-    
+
     # === Logging ===
     log_level: str = "INFO"
     log_to_file: bool = True
     progress_interval: int = 30  # seconds
     verbose_progress: bool = True
-    
+
     # === Advanced Options ===
     use_process_pool: bool = True  # vs ThreadPoolExecutor
     optimize_memory: bool = True
     cleanup_temp_files: bool = True
     validate_outputs: bool = True
-        
+
     _param_metadata: dict[str, dict[str, Any]] = field(
         default_factory=lambda: {
             "source": {
@@ -159,7 +160,7 @@ class wizard_def:
                 "required": True,
             },
             "folder": {
-                "dtype": str, 
+                "dtype": str,
                 "description": "Output directory for processed study",
                 "required": True,
             },
@@ -193,26 +194,26 @@ class wizard_def:
         },
         repr=False,
     )
-    
+
     def __post_init__(self):
         """Set polarity-specific defaults after initialization."""
         # Set default adducts based on polarity if not provided
         if not self.adducts:
             if self.polarity and self.polarity.lower() in ["positive", "pos"]:
                 self.adducts = ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"]
-            elif self.polarity and self.polarity.lower() in ["negative", "neg"]: 
+            elif self.polarity and self.polarity.lower() in ["negative", "neg"]:
                 self.adducts = ["H-1:-:1.0", "CH2O2:0:0.5"]
             else:
                 # Default to positive if polarity is None or unknown
                 self.adducts = ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"]
-        
+
         # Validate num_cores
         max_cores = multiprocessing.cpu_count()
         if self.num_cores <= 0:
             self.num_cores = max_cores
         elif self.num_cores > max_cores:
             self.num_cores = max_cores
-            
+
         # Ensure paths are absolute
         if self.source:
             self.source = os.path.abspath(self.source)
@@ -223,24 +224,24 @@ class wizard_def:
 class Wizard:
     """
     Simplified Wizard for automated mass spectrometry data processing.
-    
+
     The Wizard provides a clean interface for creating and executing analysis scripts
     that process raw MS data through the complete pipeline: file discovery, feature
     detection, sample processing, study assembly, alignment, merging, and export.
-    
+
     Core functions:
     - create_scripts(): Generate standalone analysis scripts
     - test_only(): Process only one file for parameter validation
     - test_and_run(): Test with single file, then run full batch if successful
     - run(): Execute full batch processing on all files
-    
+
     Recommended workflow:
     1. wizard = Wizard(source="raw_data", folder="output")
     2. wizard.create_scripts()  # Generate analysis scripts
     3. wizard.test_only()       # Validate with single file
     4. wizard.run()             # Process all files
     """
-    
+
     def __init__(
         self,
         source: str = "",
@@ -248,11 +249,11 @@ class Wizard:
         polarity: Optional[str] = None,
         adducts: Optional[List[str]] = None,
         num_cores: int = 6,
-        **kwargs
+        **kwargs,
     ):
         """
         Initialize the Wizard with analysis parameters.
-        
+
         Parameters:
             source: Directory containing raw data files
             folder: Output directory for processed study
@@ -261,145 +262,43 @@ class Wizard:
             num_cores: Number of CPU cores (0 = auto-detect 75% of available)
             **kwargs: Additional parameters (see wizard_def for full list)
         """
-        
+
         # Auto-detect optimal number of cores if not specified
         if num_cores <= 0:
             num_cores = max(1, int(multiprocessing.cpu_count() * 0.75))
-            
+
         # Create parameters instance
         if "params" in kwargs and isinstance(kwargs["params"], wizard_def):
             self.params = kwargs.pop("params")
         else:
             # Create default parameters
-            self.params = wizard_def(
-                source=source,
-                folder=folder,
-                polarity=polarity,
-                num_cores=num_cores
-            )
-            
+            self.params = wizard_def(source=source, folder=folder, polarity=polarity, num_cores=num_cores)
+
             # Set adducts if provided
             if adducts is not None:
                 self.params.adducts = adducts
-            
+
             # Update with any additional parameters
             for key, value in kwargs.items():
                 if hasattr(self.params, key):
                     setattr(self.params, key, value)
-        
+
         # Validate required parameters
         if not self.params.source:
             raise ValueError("source is required")
         if not self.params.folder:
             raise ValueError("folder is required")
-        
+
         # Create and validate paths
         self.source_path = Path(self.params.source)
-        self.folder_path = Path(self.params.folder) 
+        self.folder_path = Path(self.params.folder)
         self.folder_path.mkdir(parents=True, exist_ok=True)
-        
-        # Auto-infer polarity from the first file if polarity is None
-        if self.params.polarity is None:
-            inferred_polarity = self._infer_polarity_from_first_file()
-            if inferred_polarity:
-                self.params.polarity = inferred_polarity
-                # Update adducts based on inferred polarity  
-                self.params.__post_init__()
 
-    def _infer_polarity_from_first_file(self) -> str:
-        """
-        Infer polarity from the first available raw data file.
-        
-        Returns:
-            Inferred polarity string ("positive" or "negative") or "positive" as fallback
-        """
-        try:
-            # Find first file
-            for extension in ['.wiff', '.raw', '.mzML']:
-                pattern = f"**/*{extension}" if True else f"*{extension}"  # search_subfolders=True
-                files = list(self.source_path.rglob(pattern))
-                if files:
-                    first_file = files[0]
-                    break
-            else:
-                return 'positive'
-
-            # Handle different file formats
-            if first_file.suffix.lower() == '.wiff':
-                return self._infer_polarity_from_wiff(str(first_file))
-            elif first_file.suffix.lower() == '.raw':
-                return self._infer_polarity_from_raw(str(first_file))
-            elif first_file.suffix.lower() == '.mzml':
-                return self._infer_polarity_from_mzml(str(first_file))
-                    
-        except Exception:
-            # Silently fall back to default if inference fails
-            pass
-            
-        return 'positive'
-        
-    def _infer_polarity_from_wiff(self, filename: str) -> str:
-        """Infer polarity from WIFF file."""
-        try:
-            from masster.sample.load import _wiff_to_dict
-            
-            # Extract metadata from first file
-            metadata_df = _wiff_to_dict(filename)
-            
-            if not metadata_df.empty and 'polarity' in metadata_df.columns:
-                # Get polarity from first experiment  
-                first_polarity = metadata_df['polarity'].iloc[0]
-                
-                # Convert numeric polarity codes to string
-                if first_polarity == 1 or str(first_polarity).lower() in ['positive', 'pos', '+']:
-                    return "positive"
-                elif first_polarity == -1 or str(first_polarity).lower() in ['negative', 'neg', '-']:
-                    return "negative"
-        except Exception:
-            pass
-        return 'positive'
-        
-    def _infer_polarity_from_raw(self, filename: str) -> str:
-        """Infer polarity from Thermo RAW file."""
-        try:
-            from masster.sample.thermo import ThermoRawFileReader
-            
-            with ThermoRawFileReader(filename) as raw_reader:
-                # Get polarity from first scan
-                first_scan = 1
-                polarity = raw_reader.get_polarity_from_scan_event(first_scan)
-                if polarity in ['positive', 'negative']:
-                    return polarity
-        except Exception:
-            pass
-        return 'positive'
-        
-    def _infer_polarity_from_mzml(self, filename: str) -> str:
-        """Infer polarity from mzML file."""
-        try:
-            # Import pyopenms with warnings suppression
-            import warnings
-            with warnings.catch_warnings():
-                warnings.filterwarnings("ignore", message=".*OPENMS_DATA_PATH.*", category=UserWarning)
-                import pyopenms as oms
-            
-            # Load the first few spectra to check polarity
-            omsexp = oms.MSExperiment()
-            oms.MzMLFile().load(filename, omsexp)
-            
-            if omsexp.getNrSpectra() > 0:
-                first_spectrum = omsexp.getSpectra()[0]
-                try:
-                    pol = first_spectrum.getInstrumentSettings().getPolarity()
-                    if pol == 1:
-                        return "positive"
-                    elif pol == 2:
-                        return "negative"
-                except Exception:
-                    pass
-        except Exception:
-            pass
-        return 'positive'
+        # Set default polarity if not specified
+        if self.params.polarity is None:
+            self.params.polarity = "positive"
+            # Update adducts based on default polarity
+            self.params.__post_init__()
 
     @property
     def polarity(self) -> Optional[str]:
@@ -414,13 +313,13 @@ class Wizard:
     def create_scripts(self) -> Dict[str, Any]:
         """
         Generate analysis scripts based on source file analysis.
-        
+
         This method:
         1. Analyzes the source files to extract metadata
         2. Creates 1_masster_workflow.py with sample processing logic
         3. Creates 2_interactive_analysis.py marimo notebook for study exploration
         4. Returns instructions for next steps
-        
+
         Returns:
             Dictionary containing:
             - status: "success" or "error"
@@ -432,50 +331,79 @@ class Wizard:
         try:
             # Step 1: Analyze source files to extract metadata
             source_info = self._analyze_source_files()
-            
+
+            # Report extracted information from first file
+            print("\nInformation retrieval complete:")
+            print(f"  Number of files found: {source_info.get('number_of_files', 0)}")
+            print(f"  File types detected: {', '.join(source_info.get('file_types', []))}")
+            #print(f"  First file: {source_info.get('first_file', 'None')}")
+            if source_info.get('first_file'):
+                print(f"  Detected polarity: {source_info.get('polarity', 'unknown')}")
+                print(f"  Detected detector type: {source_info.get('detector_type', 'unknown')}")
+                if source_info.get('baseline', 0) > 0:
+                    print(f"  Estimated baseline intensity: {source_info.get('baseline', 0):.1f}")
+                if source_info.get('length_minutes', 0) > 0:
+                    print(f"  Run length: {source_info.get('length_minutes', 0):.1f} minutes")
+                else:
+                    print("  Run length: Could not determine")
+                if source_info.get('ms1_scans_per_second', 0) > 0:
+                    print(f"  MS1 scans per second: {source_info.get('ms1_scans_per_second', 0):.2f}")
+            print()
+
             # Update wizard parameters based on detected metadata
-            if source_info.get('polarity') and source_info['polarity'] != 'positive':
-                self.params.polarity = source_info['polarity']
-            
+            if source_info.get("polarity") and source_info["polarity"] != "positive":
+                self.params.polarity = source_info["polarity"]
+
             files_created = []
-            
+
             # Step 2: Create 1_masster_workflow.py
             workflow_script_path = self.folder_path / "1_masster_workflow.py"
+            print(f"Creating workflow script: {workflow_script_path}")
             workflow_content = self._generate_workflow_script_content(source_info)
             
             # Apply test mode modifications
             workflow_content = self._add_test_mode_support(workflow_content)
-            
-            with open(workflow_script_path, 'w', encoding='utf-8') as f:
+
+            with open(workflow_script_path, "w", encoding="utf-8") as f:
                 f.write(workflow_content)
             files_created.append(str(workflow_script_path))
-            
+
             # Step 3: Create 2_interactive_analysis.py marimo notebook
             notebook_path = self.folder_path / "2_interactive_analysis.py"
+            print(f"Creating interactive analysis notebook: {notebook_path}")
             notebook_content = self._generate_interactive_notebook_content(source_info)
-            
-            with open(notebook_path, 'w', encoding='utf-8') as f:
+
+            with open(notebook_path, "w", encoding="utf-8") as f:
                 f.write(notebook_content)
             files_created.append(str(notebook_path))
-            
+
             # Step 4: Generate instructions
             instructions = self._generate_instructions(source_info, files_created)
-            
+
             return {
                 "status": "success",
                 "message": f"Successfully created {len(files_created)} script files",
                 "instructions": instructions,
                 "files_created": files_created,
-                "source_info": source_info
+                "source_info": source_info,
             }
-            
+
         except Exception as e:
+            import traceback
+            tb = traceback.extract_tb(e.__traceback__)
+            if tb:
+                line_number = tb[-1].lineno
+                function_name = tb[-1].name
+                error_location = f" (at line {line_number} in {function_name})"
+            else:
+                error_location = ""
+            
             return {
-                "status": "error", 
-                "message": f"Failed to create scripts: {e}",
+                "status": "error",
+                "message": f"Failed to create scripts: {e}{error_location}",
                 "instructions": [],
                 "files_created": [],
-                "source_info": {}
+                "source_info": {},
             }
 
     def _analyze_source_files(self) -> Dict[str, Any]:
@@ -483,16 +411,20 @@ class Wizard:
         result = {
             "number_of_files": 0,
             "file_types": [],
-            "polarity": "positive", 
+            "detector_type": "tof",
+            "polarity": None,
+            "baseline": None,
             "length_minutes": 0.0,
-            "first_file": None
+            "ms1_scans_per_second": 0.0,            
+            "first_file": None,
+
         }
-        
+
         try:
             # Find raw data files
             extensions = [".wiff", ".raw", ".mzML"]
             raw_files = []
-            
+
             for ext in extensions:
                 pattern = f"**/*{ext}"
                 files = list(self.source_path.rglob(pattern))
@@ -500,246 +432,284 @@ class Wizard:
                     raw_files.extend(files)
                     if ext not in result["file_types"]:
                         result["file_types"].append(ext)
-            
+
             result["number_of_files"] = len(raw_files)
-            
+
             if raw_files:
                 result["first_file"] = str(raw_files[0])
-                # Simple heuristic: assume 30 minutes per file if we can't determine
-                result["length_minutes"] = 30.0
-                
+                # load first file to infer polarity and length
+                print(f"Analyzing first file: {raw_files[0]}")
+                from masster import Sample
+                sample = Sample(filename=result["first_file"], logging_level='WARNING')
+                result['polarity'] = sample.polarity
+                # take max from polars ms1_df['rt']
+                if sample.ms1_df is not None:
+                    if not sample.ms1_df.is_empty() and 'rt' in sample.ms1_df.columns:
+                        max_rt = sample.ms1_df['rt'].max()
+                        if max_rt is not None and isinstance(max_rt, (int, float)) and max_rt > 0:
+                            result["length_minutes"] = float(max_rt) / 60.0
+                            result["ms1_scans_per_second"] = len(sample.ms1_df) / float(max_rt) / 60.0
+                        
+                        baseline = sample.ms1_df['inty'].quantile(0.001)
+                        if baseline is not None and isinstance(baseline, (int, float)):
+                            result["baseline"] = float(baseline)
+                            if baseline > 5e3:
+                                result["detector_type"] = "orbitrap"
+                            else:
+                                result["detector_type"] = "tof"
+                    
         except Exception as e:
             print(f"Warning: Could not analyze source files: {e}")
-            
+
         return result
 
     def _generate_workflow_script_content(self, source_info: Dict[str, Any]) -> str:
         """Generate the content for 1_masster_workflow.py script."""
-        
+
+        # Logic 
+        noise = self.params.noise
+        if noise is None:
+            if source_info.get("detector_type") == "orbitrap":
+                noise = max(self.params.noise or 50.0, 5e4)
+            elif source_info.get("detector_type") == "tof":
+                default_noise = self.params.noise or 50.0
+                baseline = source_info.get("baseline", default_noise / 2.0)
+                noise = baseline * 2
+
+        chrom_fwhm = self.params.chrom_fwhm
+        if chrom_fwhm is None:
+            if source_info.get("length_minutes", 0) > 0:
+                if source_info["length_minutes"] < 10:
+                    chrom_fwhm = 0.5
+                else:
+                    chrom_fwhm = 2.0
+
+
+        # Generate script content     
         script_lines = [
-            '#!/usr/bin/env python3',
-            '"""',
-            'Automated Mass Spectrometry Data Analysis Pipeline',
-            'Generated by masster wizard',
+           "#!/usr/bin/env python3",
+           '"""',
+           "Automated Mass Spectrometry Data Analysis Pipeline",
+            "Generated by masster wizard",
             '"""',
-            '',
-            'import os',
-            'import sys',
-            'import time',
-            'from pathlib import Path',
-            '',
-            '# Import masster modules',
-            'from masster.study import Study',
-            'from masster import __version__',
-            '',
-            '# Test mode configuration',
-            'TEST_MODE = os.environ.get("MASSTER_TEST_MODE", "0") == "1"',
-            'TEST_ONLY = os.environ.get("MASSTER_TEST_ONLY", "0") == "1"  # Only run test, don\'t continue to full batch',
-            '',
-            '# Analysis parameters',
-            'PARAMS = {',
-            '    # === Core Configuration ===',
+            "",
+            "import os",
+            "import sys",
+            "import time",
+            "from pathlib import Path",
+            "",
+            "# Import masster modules",
+            "from masster.study import Study",
+            "from masster import __version__",
+            "",
+            "# Test mode configuration",
+            'TEST = os.environ.get("MASSTER_TEST", "0") == "1"',
+            'STOP_AFTER_TEST = os.environ.get("MASSTER_STOP_AFTER_TEST", "0") == "1"  # Only run test, don\'t continue to full batch',
+            "",
+            "# Analysis parameters",
+            "PARAMS = {",
+            "    # === Core Configuration ===",
             f'    "source": {str(self.source_path)!r},  # Directory containing raw data files',
             f'    "folder": {str(self.folder_path)!r},  # Output directory for processed study',
             f'    "polarity": {self.params.polarity!r},  # Ion polarity mode ("positive" or "negative")',
             f'    "num_cores": {self.params.num_cores},  # Number of CPU cores for parallel processing',
-            '',
-            '    # === Test Mode ===',
-            '    "test_mode": TEST_MODE,  # Process only first file for testing',
-            '    "test_only": TEST_ONLY,  # Stop after test, don\'t run full batch',
-            '',
-            '    # === File Discovery ===',
+            "",
+            "    # === Test Mode ===",
+            '    "test": TEST,  # Process only first file for testing',
+            '    "stop_after_test": STOP_AFTER_TEST,  # Stop after test, don\'t run full batch',
+            "",
+            "    # === File Discovery ===",
             f'    "file_extensions": {self.params.file_extensions!r},  # File extensions to search for',
             f'    "search_subfolders": {self.params.search_subfolders},  # Whether to search subdirectories recursively',
             f'    "skip_patterns": {self.params.skip_patterns!r},  # Filename patterns to skip',
-            '',
-            '    # === Processing Parameters ===',
+            "",
+            "    # === Processing Parameters ===",
             f'    "adducts": {self.params.adducts!r},  # Adduct specifications for feature detection and annotation',
-            f'    "noise": {self.params.noise},  # Noise threshold for feature detection',
-            f'    "chrom_fwhm": {self.params.chrom_fwhm},  # Chromatographic peak full width at half maximum (seconds)',
+            f'    "noise": {noise},  # Noise threshold for feature detection',
+            f'    "chrom_fwhm": {chrom_fwhm},  # Chromatographic peak full width at half maximum (seconds)',
             f'    "chrom_peak_snr": {self.params.chrom_peak_snr},  # Minimum signal-to-noise ratio for chromatographic peaks',
-            '',
-            '    # === Alignment & Merging ===',
+            "",
+            "    # === Alignment & Merging ===",
             f'    "rt_tol": {self.params.rt_tolerance},  # Retention time tolerance for alignment (seconds)',
             f'    "mz_tol": {self.params.mz_max_diff},  # Mass-to-charge ratio tolerance for alignment (Da)',
             f'    "alignment_method": {self.params.alignment_algorithm!r},  # Algorithm for sample alignment',
             f'    "min_samples_per_feature": {self.params.min_samples_for_merge},  # Minimum samples required per consensus feature',
             f'    "merge_method": {self.params.merge_method!r},  # Method for merging consensus features',
-            '',
-            '    # === Sample Processing (used in add_samples_from_folder) ===',
+            "",
+            "    # === Sample Processing (used in add_samples_from_folder) ===",
             f'    "batch_size": {self.params.batch_size},  # Number of files to process per batch',
             f'    "memory_limit_gb": {self.params.memory_limit_gb},  # Memory limit for processing (GB)',
-            '',
-            '    # === Script Options ===',
+            "",
+            "    # === Script Options ===",
             f'    "resume_enabled": {self.params.resume_enabled},  # Enable automatic resume capability',
             f'    "force_reprocess": {self.params.force_reprocess},  # Force reprocessing of existing files',
             f'    "cleanup_temp_files": {self.params.cleanup_temp_files},  # Clean up temporary files after processing',
-            '}',
-            '',
-            '',
-            'def discover_raw_files(source_folder, file_extensions, search_subfolders=True):',
+            "}",
+            "",
+            "",
+            "def discover_raw_files(source_folder, file_extensions, search_subfolders=True):",
             '    """Discover raw data files in the source folder."""',
-            '    source_path = Path(source_folder)',
-            '    raw_files = []',
-            '    ',
-            '    for ext in file_extensions:',
-            '        if search_subfolders:',
+            "    source_path = Path(source_folder)",
+            "    raw_files = []",
+            "    ",
+            "    for ext in file_extensions:",
+            "        if search_subfolders:",
             '            pattern = f"**/*{ext}"',
-            '            files = list(source_path.rglob(pattern))',
-            '        else:',
+            "            files = list(source_path.rglob(pattern))",
+            "        else:",
             '            pattern = f"*{ext}"',
-            '            files = list(source_path.glob(pattern))',
-            '        raw_files.extend(files)',
-            '    ',
-            '    return raw_files',
-            '',
-            '',
-            'def process_single_file(args):',
+            "            files = list(source_path.glob(pattern))",
+            "        raw_files.extend(files)",
+            "    ",
+            "    return raw_files",
+            "",
+            "",
+            "def process_single_file(args):",
             '    """Process a single raw file to sample5 format - module level for multiprocessing."""',
-            '    raw_file, output_folder = args',
-            '    from masster.sample import Sample',
-            '    ',
-            '    try:',
-            '        # Create sample5 filename',
-            '        sample_name = raw_file.stem',
+            "    raw_file, output_folder = args",
+            "    from masster.sample import Sample",
+            "    ",
+            "    try:",
+            "        # Create sample5 filename",
+            "        sample_name = raw_file.stem",
             '        sample5_path = Path(output_folder) / f"{sample_name}.sample5"',
-            '        ',
-            '        # Skip if sample5 already exists',
+            "        ",
+            "        # Skip if sample5 already exists",
             '        if sample5_path.exists() and not PARAMS["force_reprocess"]:',
             '            print(f"  Skipping {raw_file.name} (sample5 already exists)")',
-            '            return str(sample5_path)',
-            '        ',
+            "            return str(sample5_path)",
+            "        ",
             '        print(f"  Converting {raw_file.name}...")',
-            '        ',
-            '        # Load and process raw file with full pipeline',
-            '        sample = Sample(log_label=sample_name)',
-            '        sample.load(filename=str(raw_file))',
-            '        sample.find_features(',
+            "        ",
+            "        # Load and process raw file with full pipeline",
+            "        sample = Sample(log_label=sample_name)",
+            "        sample.load(filename=str(raw_file))",
+            "        sample.find_features(",
             '            noise=PARAMS["noise"],',
             '            chrom_fwhm=PARAMS["chrom_fwhm"],',
             '            chrom_peak_snr=PARAMS["chrom_peak_snr"]',
-            '        )',
-            '        sample.find_ms2()',
-            '        sample.find_iso()',
-            '        # sample.export_mgf()',
+            "        )",
+            "        sample.find_ms2()",
+            "        sample.find_iso()",
+            "        # sample.export_mgf()",
             '        # sample.plot_2d(filename=f"{sample5_path.replace(".sample5", ".html")}")',
-            '        sample.save(str(sample5_path))',
-            '        ',
+            "        sample.save(str(sample5_path))",
+            "        ",
             '        # print(f"  Completed {raw_file.name} -> {sample5_path.name}")',
-            '        return str(sample5_path)',
-            '        ',
-            '    except Exception as e:',
+            "        return str(sample5_path)",
+            "        ",
+            "    except Exception as e:",
             '        print(f"  ERROR processing {raw_file.name}: {e}")',
-            '        return None',
-            '',
-            '',
-            'def convert_raw_to_sample5(raw_files, output_folder, polarity, num_cores):',
+            "        return None",
+            "",
+            "",
+            "def convert_raw_to_sample5(raw_files, output_folder, polarity, num_cores):",
             '    """Convert raw data files to sample5 format."""',
-            '    import concurrent.futures',
-            '    import os',
-            '    ',
-            '    # Create output directory',
-            '    os.makedirs(output_folder, exist_ok=True)',
-            '    ',
-            '    # Prepare arguments for multiprocessing',
-            '    file_args = [(raw_file, output_folder) for raw_file in raw_files]',
-            '    ',
-            '    # Process files in parallel',
-            '    sample5_files = []',
-            '    with concurrent.futures.ProcessPoolExecutor(max_workers=num_cores) as executor:',
-            '        futures = [executor.submit(process_single_file, args) for args in file_args]',
-            '        ',
-            '        for future in concurrent.futures.as_completed(futures):',
-            '            result = future.result()',
-            '            if result:',
-            '                sample5_files.append(result)',
-            '    ',
-            '    return sample5_files',
-            '',
-            '',
-            'def main():',
+            "    import concurrent.futures",
+            "    import os",
+            "    ",
+            "    # Create output directory",
+            "    os.makedirs(output_folder, exist_ok=True)",
+            "    ",
+            "    # Prepare arguments for multiprocessing",
+            "    file_args = [(raw_file, output_folder) for raw_file in raw_files]",
+            "    ",
+            "    # Process files in parallel",
+            "    sample5_files = []",
+            "    with concurrent.futures.ProcessPoolExecutor(max_workers=num_cores) as executor:",
+            "        futures = [executor.submit(process_single_file, args) for args in file_args]",
+            "        ",
+            "        for future in concurrent.futures.as_completed(futures):",
+            "            result = future.result()",
+            "            if result:",
+            "                sample5_files.append(result)",
+            "    ",
+            "    return sample5_files",
+            "",
+            "",
+            "def main():",
             '    """Main analysis pipeline."""',
-            '    try:',
+            "    try:",
             '        print("=" * 70)',
             f'        print("masster {version} - Automated MS Data Analysis")',
             '        print("=" * 70)',
-            '        print(f"Source: {PARAMS[\'source\']}")',
-            '        print(f"Output: {PARAMS[\'folder\']}")',
-            '        print(f"Polarity: {PARAMS[\'polarity\']}")',
-            '        print(f"CPU Cores: {PARAMS[\'num_cores\']}")',
+            "        print(f\"Source: {PARAMS['source']}\")",
+            "        print(f\"Output: {PARAMS['folder']}\")",
+            "        print(f\"Polarity: {PARAMS['polarity']}\")",
+            "        print(f\"CPU Cores: {PARAMS['num_cores']}\")",
             '        print("=" * 70)',
-            '        ',
-            '        start_time = time.time()',
-            '        ',
-            '        # Step 1: Discover raw data files',
+            "        ",
+            "        start_time = time.time()",
+            "        ",
+            "        # Step 1: Discover raw data files",
             '        print("\\nStep 1/7: Discovering raw data files...")',
-            '        raw_files = discover_raw_files(',
-            '            PARAMS[\'source\'],',
-            '            PARAMS[\'file_extensions\'],',
-            '            PARAMS[\'search_subfolders\']',
-            '        )',
-            '        ',
-            '        if not raw_files:',
+            "        raw_files = discover_raw_files(",
+            "            PARAMS['source'],",
+            "            PARAMS['file_extensions'],",
+            "            PARAMS['search_subfolders']",
+            "        )",
+            "        ",
+            "        if not raw_files:",
             '            print("No raw data files found!")',
-            '            return False',
-            '        ',
+            "            return False",
+            "        ",
             '        print(f"Found {len(raw_files)} raw data files")',
-            '        for f in raw_files[:5]:  # Show first 5 files',
+            "        for f in raw_files[:5]:  # Show first 5 files",
             '            print(f"  {f.name}")',
-            '        if len(raw_files) > 5:',
+            "        if len(raw_files) > 5:",
             '            print(f"  ... and {len(raw_files) - 5} more")',
-            '        ',
-            '        # Step 2: Process raw files',
+            "        ",
+            "        # Step 2: Process raw files",
             '        print("\\nStep 2/7: Processing raw files...")',
-            '        sample5_files = convert_raw_to_sample5(',
-            '            raw_files,',
-            '            PARAMS[\'folder\'],',
-            '            PARAMS[\'polarity\'],',
-            '            PARAMS[\'num_cores\']',
-            '        )',
-            '        ',
-            '        if not sample5_files:',
+            "        sample5_files = convert_raw_to_sample5(",
+            "            raw_files,",
+            "            PARAMS['folder'],",
+            "            PARAMS['polarity'],",
+            "            PARAMS['num_cores']",
+            "        )",
+            "        ",
+            "        if not sample5_files:",
             '            print("No sample5 files were created!")',
-            '            return False',
-            '        ',
+            "            return False",
+            "        ",
             '        print(f"Successfully processed {len(sample5_files)} files to sample5")',
-            '        ',
-            '        # Step 3: Create and configure study',
+            "        ",
+            "        # Step 3: Create and configure study",
             '        print("\\nStep 3/7: Initializing study...")',
-            '        study = Study(folder=PARAMS[\'folder\'])',
-            '        study.polarity = PARAMS[\'polarity\']',
-            '        study.adducts = PARAMS[\'adducts\']',
-            '        ',
-            '        # Step 4: Add sample5 files to study',
+            "        study = Study(folder=PARAMS['folder'])",
+            "        study.polarity = PARAMS['polarity']",
+            "        study.adducts = PARAMS['adducts']",
+            "        ",
+            "        # Step 4: Add sample5 files to study",
             '        print("\\nStep 4/7: Adding samples to study...")',
-            '        study.add(str(Path(PARAMS[\'folder\']) / "*.sample5"))',
-            '        study.features_filter(study.features_select(chrom_coherence=0.1, chrom_prominence_scaled=1))',
-            '        ',
-            '        # Step 5: Core processing',
+            "        study.add(str(Path(PARAMS['folder']) / \"*.sample5\"))",
+            "        study.features_filter(study.features_select(chrom_coherence=0.1, chrom_prominence_scaled=1))",
+            "        ",
+            "        # Step 5: Core processing",
             '        print("\\nStep 5/7: Processing...")',
-            '        study.align(',
-            '            algorithm=PARAMS[\'alignment_method\'],',
-            '            rt_tol=PARAMS[\'rt_tol\']',
-            '        )',
-            '        ',
-            '        study.merge(',
+            "        study.align(",
+            "            algorithm=PARAMS['alignment_method'],",
+            "            rt_tol=PARAMS['rt_tol']",
+            "        )",
+            "        ",
+            "        study.merge(",
             '            method="qt",',
-            '            min_samples=PARAMS[\'min_samples_per_feature\'],',
-            '            threads=PARAMS[\'num_cores\'],',
-            '            rt_tol=PARAMS[\'rt_tol\']',
-            '        )',
-            '        study.find_iso()',
-            '        study.fill()',
-            '        study.integrate()',
-            '        ',
-            '        # Step 6/7: Saving results',
+            "            min_samples=PARAMS['min_samples_per_feature'],",
+            "            threads=PARAMS['num_cores'],",
+            "            rt_tol=PARAMS['rt_tol']",
+            "        )",
+            "        study.find_iso()",
+            "        study.fill()",
+            "        study.integrate()",
+            "        ",
+            "        # Step 6/7: Saving results",
             '        print("\\nStep 6/7: Saving results...")',
-            '        study.save()',
-            '        study.export_xlsx()',
-            '        study.export_mgf()',
-            '        study.export_mztab()',
-            '        ',
-            '        # Step 7: Plots',
+            "        study.save()",
+            "        study.export_xlsx()",
+            "        study.export_mgf()",
+            "        study.export_mztab()",
+            "        ",
+            "        # Step 7: Plots",
             '        print("\\nStep 7/7: Exporting plots...")',
             '        study.plot_consensus_2d(filename="consensus.html")',
             '        study.plot_consensus_2d(filename="consensus.png")',
@@ -751,10 +721,10 @@ class Wizard:
             '        study.plot_bpc(filename="bpc.png")',
             '        study.plot_rt_correction(filename="rt_correction.html")',
             '        study.plot_rt_correction(filename="rt_correction.png")',
-            '        ',
-            '        # Print summary',
-            '        study.info()',
-            '        total_time = time.time() - start_time',
+            "        ",
+            "        # Print summary",
+            "        study.info()",
+            "        total_time = time.time() - start_time",
             '        print("\\n" + "=" * 70)',
             '        print("ANALYSIS COMPLETE")',
             '        print("=" * 70)',
@@ -764,50 +734,50 @@ class Wizard:
             '        if hasattr(study, "consensus_df"):',
             '            print(f"Consensus features generated: {len(study.consensus_df)}")',
             '        print("=" * 70)',
-            '        ',
-            '        return True',
-            '        ',
-            '    except KeyboardInterrupt:',
+            "        ",
+            "        return True",
+            "        ",
+            "    except KeyboardInterrupt:",
             '        print("\\nAnalysis interrupted by user")',
-            '        return False',
-            '    except Exception as e:',
+            "        return False",
+            "    except Exception as e:",
             '        print(f"Analysis failed with error: {e}")',
-            '        import traceback',
-            '        traceback.print_exc()',
-            '        return False',
-            '',
-            '',
+            "        import traceback",
+            "        traceback.print_exc()",
+            "        return False",
+            "",
+            "",
             'if __name__ == "__main__":',
-            '    success = main()',
-            '    sys.exit(0 if success else 1)',
+            "    success = main()",
+            "    sys.exit(0 if success else 1)",
         ]
-        
-        return '\n'.join(script_lines)
+
+        return "\n".join(script_lines)
 
     def _generate_interactive_notebook_content(self, source_info: Dict[str, Any]) -> str:
         """Generate the content for 2_interactive_analysis.py marimo notebook."""
-        
+
         notebook_lines = [
-            'import marimo',
-            '',
+            "import marimo",
+            "",
             '__generated_with = "0.9.14"',
             'app = marimo.App(width="medium")',
-            '',
-            '@app.cell',
-            'def __():',
-            '    import marimo as mo',
-            '    return (mo,)',
-            '',
-            '@app.cell',
-            'def __(mo):',
+            "",
+            "@app.cell",
+            "def __():",
+            "    import marimo as mo",
+            "    return (mo,)",
+            "",
+            "@app.cell",
+            "def __(mo):",
             '    mo.md(r"""',
-            '    # MASSter Interactive Analysis',
-            '    ',
-            f'    **Source:** {source_info.get("number_of_files", 0)} files detected',
-            f'    **Polarity:** {source_info.get("polarity", "unknown")}',
-            '    ',
-            '    This notebook provides interactive exploration of your processed study.',
-            '    Make sure you have run `python 1_masster_workflow.py` first.',
+            "    # MASSter Interactive Analysis",
+            "    ",
+            f"    **Source:** {source_info.get('number_of_files', 0)} files detected",
+            f"    **Polarity:** {source_info.get('polarity', 'unknown')}",
+            "    ",
+            "    This notebook provides interactive exploration of your processed study.",
+            "    Make sure you have run `python 1_masster_workflow.py` first.",
             '    """)',
             '    return ()',
             '',
@@ -828,18 +798,20 @@ class Wizard:
             '    return ()',
             '',
             'if __name__ == "__main__":',
-            '    app.run()',
+            "    app.run()",
         ]
-        
-        return '\n'.join(notebook_lines)
+
+        return "\n".join(notebook_lines)
 
     def _generate_instructions(self, source_info: Dict[str, Any], files_created: List[str]) -> List[str]:
         """Generate usage instructions for the created scripts."""
-        instructions = [f"Source analysis: {source_info.get('number_of_files', 0)} files found",
+        instructions = [
+            f"Source analysis: {source_info.get('number_of_files', 0)} files found",
             f"Polarity detected: {source_info.get('polarity', 'unknown')}",
-            "Files created:"]
+            "Files created:",
+        ]
         for file_path in files_created:
-            instructions.append(f"  [OK] {str(Path(file_path).resolve())}")
+            instructions.append(f"  {str(Path(file_path).resolve())}")
         
         # Find the workflow script name from created files
         workflow_script_name = "1_masster_workflow.py"
@@ -847,7 +819,7 @@ class Wizard:
             if Path(file_path).name == "1_masster_workflow.py":
                 workflow_script_name = Path(file_path).name
                 break
-            
+
         instructions.extend([
             "",
             "Next steps:",
@@ -864,87 +836,127 @@ class Wizard:
             "",
             "4. INTERACTIVE ANALYSIS:",
             f"   uv run marimo edit {Path('2_interactive_analysis.py').name}",
-            ""]            
-        )
-        
+            "",
+        ])
+
         return instructions
 
     def _add_test_mode_support(self, workflow_content: str) -> str:
         """Add test mode functionality to the generated workflow script."""
-        lines = workflow_content.split('\n')
-        
+        lines = workflow_content.split("\n")
+
         # Insert test mode code after print statements in main function
         for i, line in enumerate(lines):
             # Add test mode print after the masster version line
             if 'print("masster' in line and 'Automated MS Data Analysis")' in line:
-                lines.insert(i + 1, '        if TEST_MODE:')
-                lines.insert(i + 2, '            print("[TEST] TEST MODE: Processing single file only")')
+                lines.insert(i + 1, '        if TEST:')
+                lines.insert(i + 2, '            print("TEST MODE: Processing single file only")')
                 break
-        
+
         # Add mode info after num_cores print
         for i, line in enumerate(lines):
-            if 'print(f"CPU Cores: {PARAMS[\'num_cores\']}")' in line:
-                lines.insert(i + 1, '        if TEST_MODE:')
-                lines.insert(i + 2, '            print(f"Mode: {\'Test Only\' if TEST_ONLY else \'Test + Full Batch\'}")')
+            if "print(f\"CPU Cores: {PARAMS['num_cores']}\")" in line:
+                lines.insert(i + 1, "        if TEST:")
+                lines.insert(i + 2, "            print(f\"Mode: {'Test Only' if STOP_AFTER_TEST else 'Test + Full Batch'}\")")
                 break
-                
+
         # Add file limitation logic after file listing
         for i, line in enumerate(lines):
             if 'print(f"  ... and {len(raw_files) - 5} more")' in line:
                 lines.insert(i + 1, '        ')
                 lines.insert(i + 2, '        # Limit to first file in test mode')
-                lines.insert(i + 3, '        if TEST_MODE:')
+                lines.insert(i + 3, '        if TEST:')
                 lines.insert(i + 4, '            raw_files = raw_files[:1]')
-                lines.insert(i + 5, '            print(f"\\n[TEST] TEST MODE: Processing only first file: {raw_files[0].name}")')
+                lines.insert(i + 5, '            print(f"\\nTEST MODE: Processing only first file: {raw_files[0].name}")')
                 break
-        
+
         # Modify num_cores for test mode
         for i, line in enumerate(lines):
-            if 'PARAMS[\'num_cores\']' in line and 'convert_raw_to_sample5(' in lines[i-2:i+3]:
-                lines[i] = line.replace('PARAMS[\'num_cores\']', 'PARAMS[\'num_cores\'] if not TEST_MODE else 1  # Use single core for test')
+            if "PARAMS['num_cores']" in line and "convert_raw_to_sample5(" in lines[i - 2 : i + 3]:
+                lines[i] = line.replace(
+                    "PARAMS['num_cores']", "PARAMS['num_cores'] if not TEST else 1  # Use single core for test"
+                )
                 break
-        
+
         # Add test-only exit logic after successful processing
         for i, line in enumerate(lines):
             if 'print(f"Successfully processed {len(sample5_files)} files to sample5")' in line:
                 lines.insert(i + 1, '        ')
-                lines.insert(i + 2, '        # Stop here if test-only mode')
-                lines.insert(i + 3, '        if TEST_ONLY:')
-                lines.insert(i + 4, '            print("\\n[TEST] TEST ONLY mode: Stopping after successful single file processing")')
+                lines.insert(i + 2, '        # Stop here if stop-after-test mode')
+                lines.insert(i + 3, '        if STOP_AFTER_TEST:')
+                lines.insert(i + 4, '            print("\\nSTOP AFTER TEST mode: Stopping after successful single file processing")')
                 lines.insert(i + 5, '            print(f"Test file created: {sample5_files[0]}")')
                 lines.insert(i + 6, '            print("\\nTo run full batch, use: wizard.run()")')
-                lines.insert(i + 7, '            total_time = time.time() - start_time')
+                lines.insert(i + 7, "            total_time = time.time() - start_time")
                 lines.insert(i + 8, '            print(f"\\nTest processing time: {total_time:.1f} seconds")')
-                lines.insert(i + 9, '            return True')
+                lines.insert(i + 9, "            return True")
                 break
-                
-        return '\n'.join(lines)
+
+        return "\n".join(lines)
 
     def test_and_run(self) -> Dict[str, Any]:
         """
         Test the sample processing workflow with a single file, then run full batch.
-        
-        This method runs the 1_masster_workflow.py script in test mode to process
-        the first raw file for validation, then automatically continues with the 
-        full batch if the test succeeds. The script must already exist - call 
+
+        This method first runs the 1_masster_workflow.py script in test-only mode to process
+        the first raw file for validation, then automatically continues with the
+        full batch if the test succeeds. The script must already exist - call
         create_scripts() first if needed.
-        
+
         Returns:
             Dictionary containing:
             - status: "success" or "error"
             - message: Status message
             - instructions: List of next steps
         """
-        return self._execute_workflow(test_mode=True)
+        # Step 1: Run test-only mode first
+        print("Step 1/2: Testing with single file...")
+        test_result = self._execute_workflow(test=True, run=False)
+        
+        if test_result["status"] != "success":
+            return {
+                "status": "error",
+                "message": f"Test failed: {test_result['message']}",
+                "instructions": [
+                    "Single file test failed",
+                    "Review parameters in 1_masster_workflow.py",
+                    "Fix issues and try again",
+                ],
+            }
+        
+        print("Test successful! Proceeding with full batch...")
+        print("Step 2/2: Processing all files...")
+        
+        # Step 2: Run full batch mode
+        full_result = self._execute_workflow(test=False, run=True)
+        
+        return full_result
 
     def test_only(self) -> Dict[str, Any]:
         """
         Test the sample processing workflow with a single file only.
-        
+
         This method runs the 1_masster_workflow.py script in test-only mode to process
         only the first raw file and then stops (does not continue to full study processing).
         The script must already exist - call create_scripts() first if needed.
-        
+
+        Returns:
+            Dictionary containing:
+            - status: "success" or "error"
+            - message: Status message
+            - instructions: List of next steps
+            - test_file: Path to the processed test file (if successful)
+        """
+        return self._execute_workflow(test=True, run=False)
+
+    def test(self) -> Dict[str, Any]:
+        """
+        Test the sample processing workflow with a single file only.
+
+        This method runs the 1_masster_workflow.py script in test-only mode to process
+        only the first raw file and then stops (does not continue to full study processing).
+        The script must already exist - call create_scripts() first if needed.
+
         Returns:
             Dictionary containing:
             - status: "success" or "error"
@@ -952,98 +964,107 @@ class Wizard:
             - instructions: List of next steps
             - test_file: Path to the processed test file (if successful)
         """
-        return self._execute_workflow(test_mode=True, test_only=True)
+        return self._execute_workflow(test=True, run=False)
+
 
     def run(self) -> Dict[str, Any]:
         """
         Run the sample processing workflow.
-        
+
         This method runs the 1_masster_workflow.py script to process raw files.
         The script must already exist - call create_scripts() first if needed.
-        
+
         Returns:
             Dictionary containing:
             - status: "success" or "error"
             - message: Status message
             - instructions: List of next steps
         """
-        return self._execute_workflow(test_mode=False)
+        return self._execute_workflow(test=False, run=True)
 
-    def _execute_workflow(self, test_mode: bool = False, test_only: bool = False) -> Dict[str, Any]:
+    def _execute_workflow(self, test: bool = False, run: bool = True) -> Dict[str, Any]:
         """
         Execute the workflow script in either test or full mode.
-        
+
         Args:
-            test_mode: If True, run in test mode (single file), otherwise full batch
-            test_only: If True, stop after single file test (only used with test_mode=True)
+            test: If True, run in test mode (single file), otherwise full batch
+            run: If False, stop after test (only used with test=True), if True continue with full processing
         """
         try:
             workflow_script_path = self.folder_path / "1_masster_workflow.py"
-            
+
             # Check if workflow script exists
             if not workflow_script_path.exists():
-                return {
-                    "status": "error",
-                    "message": "Workflow script not found. Please run create_scripts() first.",
-                    "instructions": [
-                        "[ERROR] Missing 1_masster_workflow.py",
-                        "Run: wizard.create_scripts()",
-                        "Then: wizard.run()"
-                    ]
-                }
-            
+                print("Workflow script not found. Creating scripts automatically...")
+                create_result = self.create_scripts()
+                
+                if create_result["status"] == "error":
+                    return {
+                        "status": "error",
+                        "message": f"Failed to create workflow script: {create_result['message']}",
+                        "instructions": [
+                            "Could not create 1_masster_workflow.py",
+                            "Please check source path and permissions",
+                        ],
+                    }
+                
+                print(f"Created {len(create_result.get('files_created', []))} script files")
+                for file_path in create_result.get('files_created', []):
+                    print(f"  - {file_path}")
+                print("Proceeding with workflow execution...")
+
             # Setup execution mode
-            if test_only:
+            if test and not run:
                 mode_label = "test-only"
-            elif test_mode:
+            elif test:
                 mode_label = "test"
             else:
                 mode_label = "full batch"
-                
+
             env = None
-            if test_mode:
+            if test:
                 import os
+
                 env = os.environ.copy()
-                env['MASSTER_TEST_MODE'] = '1'
-                if test_only:
-                    env['MASSTER_TEST_ONLY'] = '1'
-                
+                env["MASSTER_TEST"] = "1"
+                if not run:
+                    env["MASSTER_STOP_AFTER_TEST"] = "1"
+
             # Execute the workflow script
             print(f">> Executing {mode_label} processing workflow...")
-            print(f"[SCRIPT] Running: {workflow_script_path.name}")
+            print(f"Running: {workflow_script_path.name}")
             print("=" * 60)
-            
+
             import subprocess
-            result = subprocess.run([
-                sys.executable, str(workflow_script_path)
-            ], cwd=str(self.folder_path), env=env)
-            
+
+            result = subprocess.run([sys.executable, str(workflow_script_path)], cwd=str(self.folder_path), env=env)
+
             success = result.returncode == 0
-            
+
             if success:
                 print("=" * 60)
-                if test_only:
-                    print("[OK] Test-only processing completed successfully!")
-                    print("[INFO] Single file validated - ready for full batch")
+                if test and not run:
+                    print("Test-only processing completed successfully!")
+                    print("Single file validated - ready for full batch")
                     print("   wizard.run()")
-                elif test_mode:
-                    print("[OK] Test processing completed successfully!")
-                    print("[INFO] Next step: Run full batch")
+                elif test:
+                    print("Test processing completed successfully!")
+                    print("Next step: Run full batch")
                     print("   wizard.run()")
                 else:
-                    print("[OK] Sample processing completed successfully!")
-                    print("[INFO] Next step: Run interactive analysis")
-                    print("   uv run marimo edit 2_interactive_analysis.py")
+                    notebook_path = self.folder_path / "2_interactive_analysis.py"
+                    print("Sample processing completed successfully!")
+                    print("Next step: Run interactive analysis")
+                    print(f"   uv run marimo edit {notebook_path}")
                 print("=" * 60)
-                
-                next_step = ("Next: wizard.run()" if test_mode else 
-                           "Next: uv run marimo edit 2_interactive_analysis.py")
-                
+
+                next_step = "Next: wizard.run()" if test else f"Next: uv run marimo edit {self.folder_path / '2_interactive_analysis.py'}"
+
                 return {
                     "status": "success",
                     "message": f"{mode_label.capitalize()} processing completed successfully",
                     "instructions": [
-                        f"[OK] {mode_label.capitalize()} processing completed",
+                        f"{mode_label.capitalize()} processing completed",
                         next_step
                     ]
                 }
@@ -1052,30 +1073,30 @@ class Wizard:
                     "status": "error",
                     "message": f"Workflow execution failed with return code {result.returncode}",
                     "instructions": [
-                        "[ERROR] Check the error messages above",
+                        "Check the error messages above",
                         "Review parameters in 1_masster_workflow.py",
-                        f"Try running manually: python {workflow_script_path.name}"
-                    ]
+                        f"Try running manually: python {workflow_script_path.name}",
+                    ],
                 }
-                
+
         except Exception as e:
             return {
                 "status": "error",
                 "message": f"Failed to execute workflow: {e}",
                 "instructions": [
-                    "[ERROR] Execution failed",
+                    "Execution failed",
                     "Check that source files exist and are accessible",
-                    "Verify folder permissions"
-                ]
+                    "Verify folder permissions",
+                ],
             }
 
     def _generate_script_content(self) -> str:
         """Generate the complete analysis script content."""
-        
+
         # Convert Path objects to strings for JSON serialization
         params_dict = {}
         for key, value in self.params.__dict__.items():
-            if key == '_param_metadata':  # Skip metadata in generated script
+            if key == "_param_metadata":  # Skip metadata in generated script
                 continue
             if isinstance(value, Path):
                 params_dict[key] = str(value)
@@ -1084,251 +1105,288 @@ class Wizard:
 
         # Obtain list of files in source with extension wiff, .raw, .mzML
         raw_files = []
-        for ext in params_dict.get('file_extensions', []):
+        for ext in params_dict.get("file_extensions", []):
             raw_files.extend(glob.glob(f"{params_dict.get('source', '')}/**/*{ext}", recursive=True))
 
         # Create readable PARAMS dict with comments
         params_lines = []
-        params_lines.append('# Analysis parameters')
-        params_lines.append('PARAMS = {')
-        
+        params_lines.append("# Analysis parameters")
+        params_lines.append("PARAMS = {")
+
         # Core Configuration
-        params_lines.append('    # === Core Configuration ===')
+        params_lines.append("    # === Core Configuration ===")
         params_lines.append(f'    "source": {params_dict.get("source", "")!r},  # Directory containing raw data files')
         params_lines.append(f'    "folder": {params_dict.get("folder", "")!r},  # Output directory for processed study')
-        params_lines.append(f'    "polarity": {params_dict.get("polarity", "positive")!r},  # Ion polarity mode ("positive" or "negative")')
-        params_lines.append(f'    "num_cores": {params_dict.get("num_cores", 4)},  # Number of CPU cores for parallel processing')
-        params_lines.append('')
-        
+        params_lines.append(
+            f'    "polarity": {params_dict.get("polarity", "positive")!r},  # Ion polarity mode ("positive" or "negative")'
+        )
+        params_lines.append(
+            f'    "num_cores": {params_dict.get("num_cores", 4)},  # Number of CPU cores for parallel processing'
+        )
+        params_lines.append("")
+
         # File Discovery
-        params_lines.append('    # === File Discovery ===')
-        params_lines.append(f'    "file_extensions": {params_dict.get("file_extensions", [".wiff", ".raw", ".mzML"])!r},  # File extensions to search for')
-        params_lines.append(f'    "search_subfolders": {params_dict.get("search_subfolders", True)},  # Whether to search subdirectories recursively')
-        params_lines.append(f'    "skip_patterns": {params_dict.get("skip_patterns", ["blank", "condition"])!r},  # Filename patterns to skip')
-        params_lines.append('')
-        
+        params_lines.append("    # === File Discovery ===")
+        params_lines.append(
+            f'    "file_extensions": {params_dict.get("file_extensions", [".wiff", ".raw", ".mzML"])!r},  # File extensions to search for'
+        )
+        params_lines.append(
+            f'    "search_subfolders": {params_dict.get("search_subfolders", True)},  # Whether to search subdirectories recursively'
+        )
+        params_lines.append(
+            f'    "skip_patterns": {params_dict.get("skip_patterns", ["blank", "condition"])!r},  # Filename patterns to skip'
+        )
+        params_lines.append("")
+
         # Processing Parameters
-        params_lines.append('    # === Processing Parameters ===')
-        params_lines.append(f'    "adducts": {params_dict.get("adducts", [])!r},  # Adduct specifications for feature detection and annotation')
-        params_lines.append(f'    "detector_type": {params_dict.get("detector_type", "unknown")!r},  # MS detector type ("orbitrap", "tof", "unknown")')
+        params_lines.append("    # === Processing Parameters ===")
+        params_lines.append(
+            f'    "adducts": {params_dict.get("adducts", [])!r},  # Adduct specifications for feature detection and annotation'
+        )
+        params_lines.append(
+            f'    "detector_type": {params_dict.get("detector_type", "unknown")!r},  # MS detector type ("orbitrap", "tof", "unknown")'
+        )
         params_lines.append(f'    "noise": {params_dict.get("noise", 50.0)},  # Noise threshold for feature detection')
-        params_lines.append(f'    "chrom_fwhm": {params_dict.get("chrom_fwhm", 0.5)},  # Chromatographic peak full width at half maximum (seconds)')
-        params_lines.append(f'    "chrom_peak_snr": {params_dict.get("chrom_peak_snr", 5.0)},  # Minimum signal-to-noise ratio for chromatographic peaks')
-        params_lines.append('')
-        
+        params_lines.append(
+            f'    "chrom_fwhm": {params_dict.get("chrom_fwhm", 0.5)},  # Chromatographic peak full width at half maximum (seconds)'
+        )
+        params_lines.append(
+            f'    "chrom_peak_snr": {params_dict.get("chrom_peak_snr", 5.0)},  # Minimum signal-to-noise ratio for chromatographic peaks'
+        )
+        params_lines.append("")
+
         # Alignment & Merging
-        params_lines.append('    # === Alignment & Merging ===')
-        params_lines.append(f'    "rt_tol": {params_dict.get("rt_tol", 2.0)},  # Retention time tolerance for alignment (seconds)')
-        params_lines.append(f'    "mz_tol": {params_dict.get("mz_tol", 0.01)},  # Mass-to-charge ratio tolerance for alignment (Da)')
-        params_lines.append(f'    "alignment_method": {params_dict.get("alignment_method", "kd")!r},  # Algorithm for sample alignment')
-        params_lines.append(f'    "min_samples_per_feature": {params_dict.get("min_samples_per_feature", 1)},  # Minimum samples required per consensus feature')
-        params_lines.append(f'    "merge_method": {params_dict.get("merge_method", "qt")!r},  # Method for merging consensus features')
-        params_lines.append('')        
+        params_lines.append("    # === Alignment & Merging ===")
+        params_lines.append(
+            f'    "rt_tol": {params_dict.get("rt_tol", 2.0)},  # Retention time tolerance for alignment (seconds)'
+        )
+        params_lines.append(
+            f'    "mz_tol": {params_dict.get("mz_tol", 0.01)},  # Mass-to-charge ratio tolerance for alignment (Da)'
+        )
+        params_lines.append(
+            f'    "alignment_method": {params_dict.get("alignment_method", "kd")!r},  # Algorithm for sample alignment'
+        )
+        params_lines.append(
+            f'    "min_samples_per_feature": {params_dict.get("min_samples_per_feature", 1)},  # Minimum samples required per consensus feature'
+        )
+        params_lines.append(
+            f'    "merge_method": {params_dict.get("merge_method", "qt")!r},  # Method for merging consensus features'
+        )
+        params_lines.append("")
 
         # Sample Processing
-        params_lines.append('    # === Sample Processing (used in add_samples_from_folder) ===')
-        params_lines.append(f'    "batch_size": {params_dict.get("batch_size", 8)},  # Number of files to process per batch')
-        params_lines.append(f'    "memory_limit_gb": {params_dict.get("memory_limit_gb", 16.0)},  # Memory limit for processing (GB)')
-        params_lines.append('')        
-        
+        params_lines.append("    # === Sample Processing (used in add_samples_from_folder) ===")
+        params_lines.append(
+            f'    "batch_size": {params_dict.get("batch_size", 8)},  # Number of files to process per batch'
+        )
+        params_lines.append(
+            f'    "memory_limit_gb": {params_dict.get("memory_limit_gb", 16.0)},  # Memory limit for processing (GB)'
+        )
+        params_lines.append("")
+
         # Script Options
-        params_lines.append('    # === Script Options ===')
-        params_lines.append(f'    "resume_enabled": {params_dict.get("resume_enabled", True)},  # Enable automatic resume capability')
-        params_lines.append(f'    "force_reprocess": {params_dict.get("force_reprocess", False)},  # Force reprocessing of existing files')
-        params_lines.append(f'    "cleanup_temp_files": {params_dict.get("cleanup_temp_files", True)},  # Clean up temporary files after processing')
-        
-        params_lines.append('}')
-        
+        params_lines.append("    # === Script Options ===")
+        params_lines.append(
+            f'    "resume_enabled": {params_dict.get("resume_enabled", True)},  # Enable automatic resume capability'
+        )
+        params_lines.append(
+            f'    "force_reprocess": {params_dict.get("force_reprocess", False)},  # Force reprocessing of existing files'
+        )
+        params_lines.append(
+            f'    "cleanup_temp_files": {params_dict.get("cleanup_temp_files", True)},  # Clean up temporary files after processing'
+        )
+
+        params_lines.append("}")
+
         # Create script lines
         script_lines = [
-            '#!/usr/bin/env python3',
+            "#!/usr/bin/env python3",
             '"""',
-            'Automated Mass Spectrometry Data Analysis Pipeline',
-            f'Generated by masster wizard v{version}',
+            "Automated Mass Spectrometry Data Analysis Pipeline",
+            f"Generated by masster wizard v{version}",
             '"""',
-            '',
-            'import sys',
-            'import time',
-            'from pathlib import Path',
-            '',
-            '# Import masster modules',
-            'from masster.study import Study',
-            'from masster import __version__',
-            '',
+            "",
+            "import sys",
+            "import time",
+            "from pathlib import Path",
+            "",
+            "# Import masster modules",
+            "from masster.study import Study",
+            "from masster import __version__",
+            "",
         ]
-        
+
         # Add the formatted PARAMS
         script_lines.extend(params_lines)
-        
+
         # Add the main function and pipeline
         script_lines.extend([
-            '',
-            '',
-            'def discover_raw_files(source_folder, file_extensions, search_subfolders=True):',
+            "",
+            "",
+            "def discover_raw_files(source_folder, file_extensions, search_subfolders=True):",
             '    """Discover raw data files in the source folder."""',
-            '    source_path = Path(source_folder)',
-            '    raw_files = []',
-            '    ',
-            '    for ext in file_extensions:',
-            '        if search_subfolders:',
+            "    source_path = Path(source_folder)",
+            "    raw_files = []",
+            "    ",
+            "    for ext in file_extensions:",
+            "        if search_subfolders:",
             '            pattern = f"**/*{ext}"',
-            '            files = list(source_path.rglob(pattern))',
-            '        else:',
+            "            files = list(source_path.rglob(pattern))",
+            "        else:",
             '            pattern = f"*{ext}"',
-            '            files = list(source_path.glob(pattern))',
-            '        raw_files.extend(files)',
-            '    ',
-            '    return raw_files',
-            '',
-            '',
-            'def process_single_file(args):',
+            "            files = list(source_path.glob(pattern))",
+            "        raw_files.extend(files)",
+            "    ",
+            "    return raw_files",
+            "",
+            "",
+            "def process_single_file(args):",
             '    """Process a single raw file to sample5 format - module level for multiprocessing."""',
-            '    raw_file, output_folder = args',
-            '    from masster.sample import Sample',
-            '    ',
-            '    try:',
-            '        # Create sample5 filename',
-            '        sample_name = raw_file.stem',
+            "    raw_file, output_folder = args",
+            "    from masster.sample import Sample",
+            "    ",
+            "    try:",
+            "        # Create sample5 filename",
+            "        sample_name = raw_file.stem",
             '        sample5_path = Path(output_folder) / f"{sample_name}.sample5"',
-            '        ',
-            '        # Skip if sample5 already exists',
-            '        if sample5_path.exists():',
+            "        ",
+            "        # Skip if sample5 already exists",
+            "        if sample5_path.exists():",
             '            print(f"  Skipping {raw_file.name} (sample5 already exists)")',
-            '            return str(sample5_path)',
-            '        ',
+            "            return str(sample5_path)",
+            "        ",
             '        print(f"  Converting {raw_file.name}...")',
-            '        ',
-            '        # Load and process raw file with full pipeline',
-            '        sample = Sample(log_label=sample_name)',
-            '        sample.load(filename=str(raw_file))',
-            '        sample.find_features(',
-            '            noise=PARAMS[\'noise\'],',
-            '            chrom_fwhm=PARAMS[\'chrom_fwhm\'],',
-            '            chrom_peak_snr=PARAMS[\'chrom_peak_snr\']',
-            '        )',
-            '        sample.find_adducts(adducts=PARAMS[\'adducts\'])',
-            '        sample.find_ms2()',
-            '        # sample.find_iso()',
-            '        # sample.export_mgf()',
-            '        # sample.export_mztab()',
+            "        ",
+            "        # Load and process raw file with full pipeline",
+            "        sample = Sample(log_label=sample_name)",
+            "        sample.load(filename=str(raw_file))",
+            "        sample.find_features(",
+            "            noise=PARAMS['noise'],",
+            "            chrom_fwhm=PARAMS['chrom_fwhm'],",
+            "            chrom_peak_snr=PARAMS['chrom_peak_snr']",
+            "        )",
+            "        sample.find_adducts(adducts=PARAMS['adducts'])",
+            "        sample.find_ms2()",
+            "        sample.find_iso()",
+            "        # sample.export_mgf()",
+            "        # sample.export_mztab()",
             '        # sample.plot_2d(filename="{sample_name}.html")',
-            '        sample.save(str(sample5_path))',
-            '        ',
+            "        sample.save(str(sample5_path))",
+            "        ",
             '        # print(f"  Completed {raw_file.name} -> {sample5_path.name}")',
-            '        return str(sample5_path)',
-            '        ',
-            '    except Exception as e:',
+            "        return str(sample5_path)",
+            "        ",
+            "    except Exception as e:",
             '        print(f"  ERROR processing {raw_file.name}: {e}")',
-            '        return None',
-            '',
-            '',
-            'def convert_raw_to_sample5(raw_files, output_folder, polarity, num_cores):',
+            "        return None",
+            "",
+            "",
+            "def convert_raw_to_sample5(raw_files, output_folder, polarity, num_cores):",
             '    """Convert raw data files to sample5 format."""',
-            '    import concurrent.futures',
-            '    import os',
-            '    ',
-            '    # Create output directory',
-            '    os.makedirs(output_folder, exist_ok=True)',
-            '    ',
-            '    # Prepare arguments for multiprocessing',
-            '    file_args = [(raw_file, output_folder) for raw_file in raw_files]',
-            '    ',
-            '    # Process files in parallel',
-            '    sample5_files = []',
-            '    with concurrent.futures.ProcessPoolExecutor(max_workers=num_cores) as executor:',
-            '        futures = [executor.submit(process_single_file, args) for args in file_args]',
-            '        ',
-            '        for future in concurrent.futures.as_completed(futures):',
-            '            result = future.result()',
-            '            if result:',
-            '                sample5_files.append(result)',
-            '    ',
-            '    return sample5_files',
-            '',
-            '',
-            'def main():',
+            "    import concurrent.futures",
+            "    import os",
+            "    ",
+            "    # Create output directory",
+            "    os.makedirs(output_folder, exist_ok=True)",
+            "    ",
+            "    # Prepare arguments for multiprocessing",
+            "    file_args = [(raw_file, output_folder) for raw_file in raw_files]",
+            "    ",
+            "    # Process files in parallel",
+            "    sample5_files = []",
+            "    with concurrent.futures.ProcessPoolExecutor(max_workers=num_cores) as executor:",
+            "        futures = [executor.submit(process_single_file, args) for args in file_args]",
+            "        ",
+            "        for future in concurrent.futures.as_completed(futures):",
+            "            result = future.result()",
+            "            if result:",
+            "                sample5_files.append(result)",
+            "    ",
+            "    return sample5_files",
+            "",
+            "",
+            "def main():",
             '    """Main analysis pipeline."""',
-            '    try:',
+            "    try:",
             '        print("=" * 70)',
             f'        print("masster {version} - Automated MS Data Analysis")',
             '        print("=" * 70)',
-            '        print(f"Source: {PARAMS[\'source\']}")',
-            '        print(f"Output: {PARAMS[\'folder\']}")',
-            '        print(f"Polarity: {PARAMS[\'polarity\']}")',
-            '        print(f"CPU Cores: {PARAMS[\'num_cores\']}")',
+            "        print(f\"Source: {PARAMS['source']}\")",
+            "        print(f\"Output: {PARAMS['folder']}\")",
+            "        print(f\"Polarity: {PARAMS['polarity']}\")",
+            "        print(f\"CPU Cores: {PARAMS['num_cores']}\")",
             '        print("=" * 70)',
-            '        ',
-            '        start_time = time.time()',
-            '        ',
-            '        # Step 1: Discover raw data files',
+            "        ",
+            "        start_time = time.time()",
+            "        ",
+            "        # Step 1: Discover raw data files",
             '        print("\\nStep 1/7: Discovering raw data files...")',
-            '        raw_files = discover_raw_files(',
-            '            PARAMS[\'source\'],',
-            '            PARAMS[\'file_extensions\'],',
-            '            PARAMS[\'search_subfolders\']',
-            '        )',
-            '        ',
-            '        if not raw_files:',
+            "        raw_files = discover_raw_files(",
+            "            PARAMS['source'],",
+            "            PARAMS['file_extensions'],",
+            "            PARAMS['search_subfolders']",
+            "        )",
+            "        ",
+            "        if not raw_files:",
             '            print("No raw data files found!")',
-            '            return False',
-            '        ',
+            "            return False",
+            "        ",
             '        print(f"Found {len(raw_files)} raw data files")',
-            '        for f in raw_files[:5]:  # Show first 5 files',
+            "        for f in raw_files[:5]:  # Show first 5 files",
             '            print(f"  {f.name}")',
-            '        if len(raw_files) > 5:',
+            "        if len(raw_files) > 5:",
             '            print(f"  ... and {len(raw_files) - 5} more")',
-            '        ',
-            '        # Step 2: Process raw files',
+            "        ",
+            "        # Step 2: Process raw files",
             '        print("\\nStep 2/7: Processing raw files...")',
-            '        sample5_files = convert_raw_to_sample5(',
-            '            raw_files,',
-            '            PARAMS[\'folder\'],',
-            '            PARAMS[\'polarity\'],',
-            '            PARAMS[\'num_cores\']',
-            '        )',
-            '        ',
-            '        if not sample5_files:',
+            "        sample5_files = convert_raw_to_sample5(",
+            "            raw_files,",
+            "            PARAMS['folder'],",
+            "            PARAMS['polarity'],",
+            "            PARAMS['num_cores']",
+            "        )",
+            "        ",
+            "        if not sample5_files:",
             '            print("No sample5 files were created!")',
-            '            return False',
-            '        ',
+            "            return False",
+            "        ",
             '        print(f"Successfully processed {len(sample5_files)} files to sample5")',
-            '        ',
-            '        # Step 3: Create and configure study',
+            "        ",
+            "        # Step 3: Create and configure study",
             '        print("\\nStep 3/7: Initializing study...")',
-            '        study = Study(folder=PARAMS[\'folder\'])',
-            '        study.polarity = PARAMS[\'polarity\']',
-            '        study.adducts = PARAMS[\'adducts\']',
-            '        ',
-            '        # Step 4: Add sample5 files to study',
+            "        study = Study(folder=PARAMS['folder'])",
+            "        study.polarity = PARAMS['polarity']",
+            "        study.adducts = PARAMS['adducts']",
+            "        ",
+            "        # Step 4: Add sample5 files to study",
             '        print("\\nStep 4/7: Adding samples to study...")',
-            '        study.add(str(Path(PARAMS[\'folder\']) / "*.sample5"))',
-            '        study.features_filter(study.features_select(chrom_coherence=0.1, chrom_prominence_scaled=1))',
-            '        ',
-            '        # Step 5: Core processing',
+            "        study.add(str(Path(PARAMS['folder']) / \"*.sample5\"))",
+            "        study.features_filter(study.features_select(chrom_coherence=0.1, chrom_prominence_scaled=1))",
+            "        ",
+            "        # Step 5: Core processing",
             '        print("\\nStep 5/7: Processing...")',
-            '        study.align(',
-            '            algorithm=PARAMS[\'alignment_method\'],',
-            '            rt_tol=PARAMS[\'rt_tol\']',
-            '        )',
-            '        ',
-            '        study.merge(',
+            "        study.align(",
+            "            algorithm=PARAMS['alignment_method'],",
+            "            rt_tol=PARAMS['rt_tol']",
+            "        )",
+            "        ",
+            "        study.merge(",
             '            method="qt",',
-            '            min_samples=PARAMS[\'min_samples_per_feature\'],',
-            '            threads=PARAMS[\'num_cores\'],',
-            '            rt_tol=PARAMS[\'rt_tol\'],'
-            '        )',
-            '        study.find_iso()',
-            '        study.fill()',
-            '        study.integrate()',    
-            '        ',
-            '        # Step 6/7: Saving results',
+            "            min_samples=PARAMS['min_samples_per_feature'],",
+            "            threads=PARAMS['num_cores'],",
+            "            rt_tol=PARAMS['rt_tol'],        )",
+            "        study.find_iso()",
+            "        study.fill()",
+            "        study.integrate()",
+            "        ",
+            "        # Step 6/7: Saving results",
             '        print("\\nStep 6/7: Saving results...")',
-            '        study.save()',
-            '        study.export_xlsx()',
-            '        study.export_mgf()',
-            '        study.export_mztab()',
-            '        ',
-            '        # Step 7: Plots',
+            "        study.save()",
+            "        study.export_xlsx()",
+            "        study.export_mgf()",
+            "        study.export_mztab()",
+            "        ",
+            "        # Step 7: Plots",
             '        print("\\nStep 7/7: Exporting plots...")',
             '        study.plot_consensus_2d(filename="consensus.html")',
             '        study.plot_consensus_2d(filename="consensus.png")',
@@ -1340,11 +1398,10 @@ class Wizard:
             '        study.plot_bpc(filename="bpc.png")',
             '        study.plot_rt_correction(filename="rt_correction.html")',
             '        study.plot_rt_correction(filename="rt_correction.png")',
-
-            '        ',
-            '        # Print summary',
-            '        study.info()',
-            '        total_time = time.time() - start_time',
+            "        ",
+            "        # Print summary",
+            "        study.info()",
+            "        total_time = time.time() - start_time",
             '        print("\\n" + "=" * 70)',
             '        print("ANALYSIS COMPLETE")',
             '        print("=" * 70)',
@@ -1354,41 +1411,41 @@ class Wizard:
             '        if hasattr(study, "consensus_df"):',
             '            print(f"Consensus features generated: {len(study.consensus_df)}")',
             '        print("=" * 70)',
-            '        ',
-            '        return True',
-            '        ',
-            '    except KeyboardInterrupt:',
+            "        ",
+            "        return True",
+            "        ",
+            "    except KeyboardInterrupt:",
             '        print("\\nAnalysis interrupted by user")',
-            '        return False',
-            '    except Exception as e:',
+            "        return False",
+            "    except Exception as e:",
             '        print(f"Analysis failed with error: {e}")',
-            '        import traceback',
-            '        traceback.print_exc()',
-            '        return False',
-            '',
-            '',
+            "        import traceback",
+            "        traceback.print_exc()",
+            "        return False",
+            "",
+            "",
             'if __name__ == "__main__":',
-            '    success = main()',
-            '    sys.exit(0 if success else 1)',
+            "    success = main()",
+            "    sys.exit(0 if success else 1)",
         ])
-        
-        return '\n'.join(script_lines)
+
+        return "\n".join(script_lines)
 
 
 def create_scripts(
-    source: str = "", 
-    folder: str = "", 
+    source: str = "",
+    folder: str = "",
     polarity: Optional[str] = None,
     adducts: Optional[List[str]] = None,
     num_cores: int = 0,
-    **kwargs
+    **kwargs,
 ) -> Dict[str, Any]:
     """
     Create analysis scripts without explicitly instantiating a Wizard.
-    
+
     This is a convenience function that creates a Wizard instance internally
     and calls its create_scripts() method.
-    
+
     Parameters:
         source: Directory containing raw data files
         folder: Output directory for processed study
@@ -1396,7 +1453,7 @@ def create_scripts(
         adducts: List of adduct specifications (auto-set if None)
         num_cores: Number of CPU cores (0 = auto-detect)
         **kwargs: Additional parameters
-        
+
     Returns:
         Dictionary containing:
         - status: "success" or "error"
@@ -1404,42 +1461,35 @@ def create_scripts(
         - instructions: List of next steps
         - files_created: List of created file paths
         - source_info: Metadata about source files
-        
+
     Example:
         >>> import masster.wizard
         >>> result = masster.wizard.create_scripts(
         ...     source=r'D:\\Data\\raw_files',
-        ...     folder=r'D:\\Data\\output', 
+        ...     folder=r'D:\\Data\\output',
         ...     polarity='negative'
         ... )
         >>> print("Status:", result["status"])
     """
-    
+
     try:
         # Auto-detect optimal number of cores if not specified
         if num_cores <= 0:
             num_cores = max(1, int(multiprocessing.cpu_count() * 0.75))
-        
+
         # Create Wizard instance
-        wizard = Wizard(
-            source=source,
-            folder=folder,
-            polarity=polarity,
-            adducts=adducts,
-            num_cores=num_cores,
-            **kwargs
-        )
-        
+        wizard = Wizard(source=source, folder=folder, polarity=polarity, adducts=adducts, num_cores=num_cores, **kwargs)
+
         # Call the instance method
         return wizard.create_scripts()
-        
+
     except Exception as e:
         return {
             "status": "error",
             "message": f"Failed to create scripts: {e}",
             "instructions": [],
             "files_created": [],
-            "source_info": {}
+            "source_info": {},
         }