masster 0.4.20__py3-none-any.whl → 0.4.22__py3-none-any.whl

{masster-0.4.20.dist-info → masster-0.4.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.20
+Version: 0.4.22
 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-0.4.20.dist-info → masster-0.4.22.dist-info}/RECORD

@@ -1,8 +1,8 @@
-masster/__init__.py,sha256=Btr_yVIY2S4gI0t5f2ZgIRFPiBBDJOq9Jqf9lh8PWx4,775
-masster/_version.py,sha256=nrWkv_1h3nB0Kn1uxpIVJdwPz73mGUWmFDSEREXTW4Y,257
+masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
+masster/_version.py,sha256=vQFUBi9UR5DFflCbwobRTLg-jW9TsSQB1GlM1tfxYuc,257
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=tR65N23zfrNpcZNbZm2ot_Aual9XrGB1MWjLrovZkMs,16749
-masster/spectrum.py,sha256=_upC_g2N9gwTaflXAugs9pSXpKUmzbIehofDordk7WI,47718
+masster/spectrum.py,sha256=XJSUrqXZSzfpWnD8v5IMClXMRZLKLYIk014qaMOS9_k,49738
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil2_01_20250602151849.sample5,sha256=LdJMF8uLoDm9ixZNHBoOzBH6hX7NGY7vTvqa2Pzetb8,6539174
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil3_01_20250602150634.sample5,sha256=hWUfslGoOTiQw59jENSBXP4sa6DdkbOi40FJ68ep61Q,6956773
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v6_r38_01.sample5,sha256=dSd2cIgYYdRcNSzkhqlZCeWKi3x8Hhhcx8BFMuiVG4c,11382948
@@ -18,17 +18,17 @@ masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
 masster/lib/lib.py,sha256=mxUYBCBmkSBZB82557smSHCS25BAusuCewvW8zwsLGg,27130
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
 masster/sample/adducts.py,sha256=jdtkkiMFeObRv3myluUx--IfpRsEq3-hPgkCb2VUxy4,32590
-masster/sample/h5.py,sha256=7NJeErlIHwC2Qh3nchusLZJWjBGue9zExAx08C89qhg,111889
+masster/sample/h5.py,sha256=B0gAmhrnoFoybotqsqiT8s-PkeZWUdIQfI-4cnM52Zc,115430
 masster/sample/helpers.py,sha256=JhzFpNh7j7YVUibIMuPQ50hBcGDEBCaBbmwA3Z5OhgM,41336
 masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
-masster/sample/load.py,sha256=Hc0ZZWZS719JOdDmx-NaPP1yHKf_peSoBpbNRUz2UfA,51168
+masster/sample/load.py,sha256=TqBuDPrNgIotR-mL475AfDZntsW0JjYcy5AovVKRZxY,51560
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
-masster/sample/plot.py,sha256=abLnG0Bk75vqSGQz6uA3uTK3IE9N-s687ZH-n8Mhdzg,82757
-masster/sample/processing.py,sha256=lCHRv290oAFOxe_zR5GMi4FdxodjJh1rj2uLWy_wHnc,49771
+masster/sample/plot.py,sha256=bQlEXCLQQWpUV88vGtftW9WAVwDKZ4k7TBirV9cO54w,82573
+masster/sample/processing.py,sha256=A1u5u7lGG0HR_ciUhJFmmwgugher7_AZQopNnbu65Bs,55910
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=uibBjBlH97CP7Mx8HoFdmHMj6Re_vvHUuaYmlp5TEmI,19715
-masster/sample/sample5_schema.json,sha256=voVB6z0TaIJwU-_SPUEYWKH7mKC16ycTe1nW6gODYP8,3916
-masster/sample/save.py,sha256=XZl5ITYdOjojYFOoUZ-0ygVSPH1kT5Va6e8NyuTRNAI,32500
+masster/sample/sample.py,sha256=uQP5DLdsRSC2YwZZvspsL9rgl_HefB-oxrL2dpgg_fc,19788
+masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
+masster/sample/save.py,sha256=2yQtcQcRJjgAKPImTydj7LpyyMop_Q9JKRlNEK4yU6k,36339
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
@@ -37,18 +37,18 @@ masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeB
 masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
 masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
 masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
-masster/study/export.py,sha256=L-YOUGSgVeTprYnrQxaN0qC8MRqUdDQ0D4o2h7HLi2Q,54813
-masster/study/h5.py,sha256=LiVGUAtULyPpZIUmKVJSaV38huJb8FsKOUWBOqiv0QU,82363
-masster/study/helpers.py,sha256=UJgwMBvkhiMHV1XAn2qtGVaaBPW_r7P7Mv0uoyqRbCs,160219
+masster/study/export.py,sha256=c-UQPYRwNBde8E1cYOB-0ZZz2tBDTwglRMlPfSKYB0w,59291
+masster/study/h5.py,sha256=eINlVmcJuntwbkkZHwzm10c63Kg7zib49vkzLDj1PyU,84790
+masster/study/helpers.py,sha256=6nDTNlsZbZWf9L6D5qzK2TUO2y7UBq51Ftj8N4bkIAk,160260
 masster/study/id.py,sha256=6NUBBKZCFOU1wlDKM0eXQeOIStSZCRNJ_3x7ZaIHzmM,55263
-masster/study/load.py,sha256=CQQY_7BzagE3oQTdDlqNyfuMdVWIAft-M4a2WCFnxp0,70695
-masster/study/merge.py,sha256=39RA7kpok1nlfYsXKpNqETdxJnv2H0TtyexV2nkSgoc,158699
+masster/study/load.py,sha256=mI6UyErlj3vIzSuG93fOjsxA7IIDCaiKfcuAcc2538o,72425
+masster/study/merge.py,sha256=3R_Dg6l2mnJUu3gFVAgrAN5hFSQyfHbqYPmc2cUfJqQ,159232
 masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
-masster/study/plot.py,sha256=OW_9d6hp4Oq1B9qpZHSU-wO-AkAmmGSZZfUIvLMpwk0,88629
-masster/study/processing.py,sha256=u1MSRKTzcqHNz_dClSUSfgTxkNRdBLXtVyO5LXuW_uk,41031
-masster/study/save.py,sha256=YCvp4xhnG16sNXaT2mFDBoCrIMub0Es61B97qLo0maw,6705
-masster/study/study.py,sha256=UX07uyCEzdLSHJvp6bxavrNsd5m5zqkzTTCAc7QM5P8,39694
-masster/study/study5_schema.json,sha256=c0w24QdHak01m04I1VPu97KvF2468FcaqROhf6pmLk4,7507
+masster/study/plot.py,sha256=OGUa_dDTD2QydbLg-4APRZc7Jx1kk9eXC9-GOLLgI1I,87666
+masster/study/processing.py,sha256=p0d-DyxA0YI6K9OPQZYTEs00DC6obr6-kLHPVWljEO0,56437
+masster/study/save.py,sha256=BANh9F1s-q7MclO1Mq_-v4xQyHeloEgmoPgRDVc-9aE,9037
+masster/study/study.py,sha256=rk-pJNg80N6xbROa9fqPfwVxFgzL_FLoSUNOTYeD5E0,40116
+masster/study/study5_schema.json,sha256=ghBeAXFS4a4Uavdn6TUVs9GaR1QOTnADCjQTOkN0tjU,7563
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=hHQbGgsOqMRHHr0Wn8Onr8XeaRz3-fFE0qGE-OMst80,20324
 masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8IJULXeWo,1203
@@ -62,13 +62,11 @@ masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgP
 masster/study/defaults/merge_def.py,sha256=K7sfwEGfgcWU85zorbWNFaxDhqRH52pxQoKv9Jn2qhY,15030
 masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7it5pL0,16033
 masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,14149
-masster/wizard/__init__.py,sha256=Jw585YKI02VabRKUG8PhyU-lBqceZK_TIl4WBS4dvlM,530
+masster/wizard/__init__.py,sha256=a2hcZnHASjfuw1lqZhZnvTR58rc33rRnoGAY_JfvGhI,683
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
-masster/wizard/test_structure.py,sha256=h88gsYYCG6iDRjqPZC_r1H1T8y79j0E-K6OrwuHaSCU,1586
-masster/wizard/test_wizard.py,sha256=CMp1cpjH3iYYC5Fy6puF_K0kfwwk3bgOsSbUGW-t7Xk,8986
-masster/wizard/wizard.py,sha256=wVm0QJnV7am5gBxVUrqXX2UIZehnD1bq1C1mohLrsZ4,105884
-masster-0.4.20.dist-info/METADATA,sha256=8l19L39xZFXnBteH7thb8cZXl8jd1mfx8o2S6KKVyac,44207
-masster-0.4.20.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.4.20.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.4.20.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.4.20.dist-info/RECORD,,
+masster/wizard/wizard.py,sha256=esgaifLRyaGxytif9qOkTy-21VxlUQxrvl47K-l-BpE,37666
+masster-0.4.22.dist-info/METADATA,sha256=CXrrzzCC5cZ_G9plLZyCtiNpTXevD0wPuUNm0mIy-a4,44207
+masster-0.4.22.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.4.22.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.4.22.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.4.22.dist-info/RECORD,,

masster/wizard/test_structure.py

@@ -1,49 +0,0 @@
-#!/usr/bin/env python3
-"""
-Simple test to verify the wizard module structure works correctly.
-"""
-
-def test_wizard_module_import():
-    """Test that the wizard module can be imported."""
-    try:
-        # Test direct wizard module import
-        import sys
-        from pathlib import Path
-        
-        # Add the masster directory to path
-        masster_path = Path(__file__).parent.parent
-        sys.path.insert(0, str(masster_path))
-        
-        # Import wizard directly from its module
-        from wizard import Wizard, wizard_def
-        
-        print("✅ Successfully imported Wizard from wizard module")
-        print(f"✅ wizard_def class available: {wizard_def}")
-        print(f"✅ Wizard class available: {Wizard}")
-        
-        # Test creating wizard_def instance
-        defaults = wizard_def(
-            data_source="/test/data",
-            study_folder="/test/output",
-            polarity="positive"
-        )
-        
-        print(f"✅ Created wizard_def instance with polarity: {defaults.polarity}")
-        print(f"✅ Default adducts: {defaults.adducts}")
-        
-        return True
-        
-    except Exception as e:
-        print(f"❌ Import failed: {e}")
-        import traceback
-        traceback.print_exc()
-        return False
-
-if __name__ == "__main__":
-    success = test_wizard_module_import()
-    print("\n" + "="*50)
-    if success:
-        print("🎉 WIZARD MODULE STRUCTURE TEST PASSED!")
-    else:
-        print("❌ WIZARD MODULE STRUCTURE TEST FAILED!")
-    print("="*50)

masster/wizard/test_wizard.py

@@ -1,285 +0,0 @@
-#!/usr/bin/env python3
-"""
-Test script for the Wizard class.
-
-This script tests the basic functionality of the Wizard class without
-requiring actual raw data files.
-"""
-
-import tempfile
-from pathlib import Path
-import sys
-
-# Add masster to path if needed
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from masster import Wizard, wizard_def
-
-
-def test_wizard_initialization():
-    """Test wizard initialization and parameter handling."""
-    print("Testing Wizard initialization...")
-    
-    with tempfile.TemporaryDirectory() as temp_dir:
-        temp_path = Path(temp_dir)
-        data_source = temp_path / "data"
-        study_folder = temp_path / "study"
-        
-        # Create directories
-        data_source.mkdir()
-        
-        # Test basic initialization
-        wizard = Wizard(
-            data_source=str(data_source),
-            study_folder=str(study_folder),
-            polarity="positive",
-            num_cores=2
-        )
-        
-        assert wizard.polarity == "positive"
-        assert wizard.params.num_cores == 2
-        assert len(wizard.adducts) > 0  # Should have default adducts
-        assert study_folder.exists()  # Should create output directory
-        
-        print("✅ Basic initialization works")
-        
-        # Test parameter validation
-        try:
-            Wizard(
-                data_source="",  # Empty data source should fail
-                study_folder=str(study_folder)
-            )
-            assert False, "Should have failed with empty data_source"
-        except ValueError:
-            print("✅ Parameter validation works")
-        
-        # Test custom parameters
-        custom_params = wizard_def(
-            data_source=str(data_source),
-            study_folder=str(study_folder / "custom"),
-            polarity="negative",
-            num_cores=4,
-            adducts=["H-1:-:1.0", "Cl:-:0.1"],
-            batch_size=2,
-            generate_plots=False
-        )
-        
-        custom_wizard = Wizard(params=custom_params)
-        assert custom_wizard.polarity == "negative"
-        assert custom_wizard.params.batch_size == 2
-        assert not custom_wizard.params.generate_plots
-        
-        print("✅ Custom parameters work")
-
-
-def test_file_discovery():
-    """Test file discovery functionality."""
-    print("\nTesting file discovery...")
-    
-    with tempfile.TemporaryDirectory() as temp_dir:
-        temp_path = Path(temp_dir)
-        data_source = temp_path / "data"
-        study_folder = temp_path / "study"
-        
-        # Create test directory structure
-        data_source.mkdir()
-        (data_source / "subdir").mkdir()
-        
-        # Create mock files
-        test_files = [
-            "sample1.wiff",
-            "sample2.raw", 
-            "sample3.mzML",
-            "blank.wiff",  # Should be skipped
-            "QC_test.raw",  # Should be skipped
-            "subdir/sample4.wiff",
-        ]
-        
-        for filename in test_files:
-            file_path = data_source / filename
-            file_path.parent.mkdir(parents=True, exist_ok=True)
-            file_path.write_text("mock file content")
-        
-        # Create wizard
-        wizard = Wizard(
-            data_source=str(data_source),
-            study_folder=str(study_folder),
-            polarity="positive"
-        )
-        
-        # Test file discovery
-        found_files = wizard.discover_files()
-        found_names = [f.name for f in found_files]
-        
-        # Should find sample files but skip blanks and QC
-        assert "sample1.wiff" in found_names
-        assert "sample2.raw" in found_names
-        assert "sample3.mzML" in found_names
-        assert "sample4.wiff" in found_names  # From subdirectory
-        assert "blank.wiff" not in found_names  # Should be skipped
-        assert "QC_test.raw" not in found_names  # Should be skipped
-        
-        print(f"✅ Found {len(found_files)} files, correctly filtered")
-        
-        # Test without subdirectory search
-        wizard.params.search_subfolders = False
-        found_files_no_sub = wizard.discover_files()
-        found_names_no_sub = [f.name for f in found_files_no_sub]
-        
-        assert "sample4.wiff" not in found_names_no_sub  # Should not find in subdir
-        assert len(found_files_no_sub) < len(found_files)
-        
-        print("✅ Subdirectory search control works")
-
-
-def test_wizard_status():
-    """Test status monitoring and checkpointing."""
-    print("\nTesting status monitoring...")
-    
-    with tempfile.TemporaryDirectory() as temp_dir:
-        temp_path = Path(temp_dir)
-        data_source = temp_path / "data"
-        study_folder = temp_path / "study"
-        
-        data_source.mkdir()
-        
-        wizard = Wizard(
-            data_source=str(data_source),
-            study_folder=str(study_folder),
-            polarity="positive"
-        )
-        
-        # Test initial status
-        status = wizard.get_status()
-        assert status["current_step"] == "initialized"
-        assert status["processed_files"] == 0
-        assert not status["study_loaded"]
-        
-        print("✅ Initial status correct")
-        
-        # Test status update
-        wizard.current_step = "converting_to_sample5"
-        wizard.processed_files = ["file1.wiff", "file2.raw"]
-        
-        status = wizard.get_status()
-        assert status["current_step"] == "converting_to_sample5"
-        assert status["processed_files"] == 2
-        
-        print("✅ Status updates work")
-        
-        # Test checkpoint save/load
-        wizard._save_checkpoint()
-        checkpoint_file = wizard.checkpoint_file
-        assert checkpoint_file.exists()
-        
-        print("✅ Checkpoint saving works")
-        
-        # Create new wizard and test checkpoint loading
-        new_wizard = Wizard(
-            data_source=str(data_source),
-            study_folder=str(study_folder),
-            polarity="positive",
-            resume_enabled=True
-        )
-        
-        # Should load from checkpoint
-        assert len(new_wizard.processed_files) == 2
-        assert new_wizard.current_step == "converting_to_sample5"
-        
-        print("✅ Checkpoint loading works")
-
-
-def test_defaults_and_validation():
-    """Test default parameter classes and validation."""
-    print("\nTesting parameter defaults and validation...")
-    
-    # Test wizard_def defaults
-    defaults = wizard_def()
-    
-    # Should set polarity-specific adducts
-    assert len(defaults.adducts) > 0
-    
-    # Test polarity switching
-    neg_defaults = wizard_def(polarity="negative")
-    pos_defaults = wizard_def(polarity="positive")
-    
-    # Should have different adducts
-    assert neg_defaults.adducts != pos_defaults.adducts
-    
-    print("✅ Polarity-specific defaults work")
-    
-    # Test parameter validation
-    defaults = wizard_def(
-        data_source="/test/path",
-        study_folder="/test/output",
-        num_cores=999  # Should be capped to available cores
-    )
-    
-    import multiprocessing
-    max_cores = multiprocessing.cpu_count()
-    assert defaults.num_cores <= max_cores
-    
-    print("✅ Parameter validation works")
-
-
-def test_logging_setup():
-    """Test logging configuration."""
-    print("\nTesting logging setup...")
-    
-    with tempfile.TemporaryDirectory() as temp_dir:
-        temp_path = Path(temp_dir)
-        data_source = temp_path / "data"
-        study_folder = temp_path / "study"
-        
-        data_source.mkdir()
-        
-        wizard = Wizard(
-            data_source=str(data_source),
-            study_folder=str(study_folder),
-            polarity="positive",
-            log_to_file=True,
-            log_level="DEBUG"
-        )
-        
-        # Test logging
-        wizard._log_progress("Test message")
-        
-        # Check log files exist
-        assert wizard.log_file.exists()
-        
-        # Check log content
-        log_content = wizard.log_file.read_text()
-        assert "Test message" in log_content
-        
-        print("✅ Logging setup works")
-
-
-def main():
-    """Run all tests."""
-    print("=" * 50)
-    print("WIZARD CLASS TESTS")
-    print("=" * 50)
-    
-    try:
-        test_wizard_initialization()
-        test_file_discovery()
-        test_wizard_status()
-        test_defaults_and_validation()
-        test_logging_setup()
-        
-        print("\n" + "=" * 50)
-        print("🎉 ALL TESTS PASSED!")
-        print("=" * 50)
-        
-    except Exception as e:
-        print(f"\n❌ TEST FAILED: {e}")
-        import traceback
-        traceback.print_exc()
-        return False
-    
-    return True
-
-
-if __name__ == "__main__":
-    success = main()
-    sys.exit(0 if success else 1)