masster 0.6.3__tar.gz → 0.6.4__tar.gz

{masster-0.6.3 → masster-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.6.3
+Version: 0.6.4
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.6.3 → masster-0.6.4}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.6.3"
+version = "0.6.4"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab, ETH Zurich" }

{masster-0.6.3 → masster-0.6.4}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.6.3"
+__version__ = "0.6.4"
 
 
 def get_version():

{masster-0.6.3 → masster-0.6.4}/src/masster/wizard/wizard.py

@@ -47,11 +47,7 @@ from dataclasses import dataclass, field
 import concurrent.futures
 from datetime import datetime
 
-# Import masster modules - use delayed import to avoid circular dependencies
-from masster.logger import MassterLogger
 from masster.study.defaults.study_def import study_defaults
-from masster.study.defaults.align_def import align_defaults
-from masster.study.defaults.merge_def import merge_defaults
 from masster._version import __version__ as version
 
 
@@ -466,6 +462,12 @@ class Wizard:
     def _generate_workflow_script_content(self, source_info: Dict[str, Any]) -> str:
         """Generate the content for 1_masster_workflow.py script."""
 
+        # Get default adducts for both polarities from study_defaults
+        pos_defaults = study_defaults(polarity="positive")
+        neg_defaults = study_defaults(polarity="negative")
+        adducts_pos = pos_defaults.adducts
+        adducts_neg = neg_defaults.adducts
+
         # Logic 
         noise = self.params.noise
         if noise is None:
@@ -499,7 +501,7 @@ class Wizard:
             "from pathlib import Path",
             "",
             "# Import masster modules",
-            "from masster.study import Study",
+            "from masster import Study",
             "from masster import __version__",
             "",
             "# Test mode configuration",
@@ -524,7 +526,8 @@ class Wizard:
             f'    "skip_patterns": {self.params.skip_patterns!r},  # Filename patterns to skip',
             "",
             "    # === Processing Parameters ===",
-            f'    "adducts": {self.params.adducts!r},  # Adduct specifications for feature detection and annotation',
+            f'    "adducts_pos": {adducts_pos!r},  # Adduct specifications for positive polarity',
+            f'    "adducts_neg": {adducts_neg!r},  # Adduct specifications for negative polarity',
             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',
@@ -567,7 +570,7 @@ class Wizard:
             "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",
+            "    from masster import Sample",
             "    ",
             "    try:",
             "        # Create sample5 filename",
@@ -676,7 +679,9 @@ class Wizard:
             "        ",
             "        # Step 3: Create and configure study",
             '        print("\\nStep 3/7: Initializing study...")',
-            "        study = Study(folder=PARAMS['folder'], polarity=PARAMS['polarity'], adducts=PARAMS['adducts'])",
+            "        # Select adducts based on polarity",
+            "        adducts = PARAMS['adducts_pos'] if PARAMS['polarity'] in ['positive', 'pos', '+'] else PARAMS['adducts_neg']",
+            "        study = Study(folder=PARAMS['folder'], polarity=PARAMS['polarity'], adducts=adducts)",
             "        ",
             "        # Step 4: Add sample5 files to study",
             '        print("\\nStep 4/7: Adding samples to study...")',