masster 0.6.3__py3-none-any.whl → 0.6.4__py3-none-any.whl

masster/_version.py

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

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...")',

{masster-0.6.3.dist-info → masster-0.6.4.dist-info}/METADATA

@@ -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.dist-info → masster-0.6.4.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=B7zftzdElF2Wb5B7KvkD6TONnMIY-Jxeen3s49dgmzs,1029
-masster/_version.py,sha256=F5yXPDNAH_yxh-afUbD7lHwHIQszYzcte4_cj7i1mFw,256
+masster/_version.py,sha256=fri37SFotav6MlUP5Xnl47Jc0GzPXzNXzlcUizkDbAo,256
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=MbQ3uLI3N0G3tnvtGIJZN_HEwjKRfIhBVZmIzUev7oc,18827
 masster/spectrum.py,sha256=LlmxrI5MFS3aPrGSdqUSKVY0rJnKeBh3Frdh6a4dPvA,49722
@@ -61,9 +61,9 @@ masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgP
 masster/study/defaults/merge_def.py,sha256=99TJtIk7mSoq8NMJMJ4b-cy7gUUixQN69krxttBnkfA,12899
 masster/study/defaults/study_def.py,sha256=kSvhiqpFp8b84vUsE8608LQsSXwz9lAPcU2BqK0T8z0,16095
 masster/wizard/__init__.py,sha256=L9G_datyGSFJjrBVklEVpZVLGXzUhDiWobtiygBH8vQ,669
-masster/wizard/wizard.py,sha256=YVmq-rCMhTzztq-GPdDmAkgQFHwOpdrWYDNOZ8VaVJw,66606
-masster-0.6.3.dist-info/METADATA,sha256=QrY0P0Ab3IXtBqq6wJGUBEir3fHe2-8TFhMuRpF7sic,50818
-masster-0.6.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.6.3.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.6.3.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.6.3.dist-info/RECORD,,
+masster/wizard/wizard.py,sha256=OO_tQC9yDXlCYwzrriakoka73E2XtudroruiU39bMWM,66895
+masster-0.6.4.dist-info/METADATA,sha256=9wZmkmfO-5-CvwYPTOlBdNz4IldHvJ23Vbtemx78sBk,50818
+masster-0.6.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.6.4.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.6.4.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.6.4.dist-info/RECORD,,