masster 0.4.10__py3-none-any.whl → 0.4.12__py3-none-any.whl

masster/study/processing.py

@@ -829,6 +829,11 @@ def merge(self, **kwargs):
                 "adduct_mass_shift_top": round(adduct_mass_shift_top, 6)
                 if adduct_mass_shift_top is not None
                 else None,
+                # New columns for top-scoring identification results
+                "id_top_name": None,
+                "id_top_class": None,
+                "id_top_adduct": None,
+                "id_top_score": None,
             },
         )
 

masster/study/study.py

@@ -338,6 +338,7 @@ class Study:
 
         # Library DataFrame (populated by lib_load)
         self.lib_df = pl.DataFrame()
+
         # Identification results DataFrame (populated by identify)
         self.id_df = pl.DataFrame()
 
@@ -358,53 +359,44 @@ class Study:
         # cache for Sample instances created/loaded by this Study
         self._samples_cache = {}
 
-    # Attach module functions as class methods
+    # ===== ATTACH MODULE FUNCTIONS AS CLASS METHODS =====
+    
+    # === File I/O Operations ===
     load = load
     save = save
     save_consensus = save_consensus
     save_samples = save_samples
+    sanitize = sanitize
+    set_folder = set_folder
+    
+    # === Sample Management ===
+    add = add
+    add_folder = add  # backward compatibility alias
+    add_sample = add_sample
+    
+    # === Core Processing Operations ===
     align = align
-    fill_single = fill_single
-    fill_chrom_single = fill_single  # Backward compatibility alias
     merge = merge
     find_consensus = merge  # Backward compatibility alias
     find_ms2 = find_ms2
     integrate = integrate
     integrate_chrom = integrate  # Backward compatibility alias
-    store_history = store_history
-    get_parameters = get_parameters
-    update_parameters = update_parameters
-    get_parameters_property = get_parameters_property
-    set_parameters_property = set_parameters_property
-    plot_alignment = plot_alignment
-    plot_chrom = plot_chrom
-    plot_consensus_2d = plot_consensus_2d
-    plot_consensus_stats = plot_consensus_stats
-    plot_pca = plot_pca
-    plot_samples_2d = plot_samples_2d
-    plot_bpc = plot_bpc
-    plot_rt_correction = plot_rt_correction
-    plot_tic = plot_tic
-    plot_eic = plot_eic
+    fill = fill
+    fill_chrom = fill  # Backward compatibility alias
+    fill_single = fill_single
+    fill_chrom_single = fill_single  # Backward compatibility alias
+    
+    # === Data Retrieval and Access ===
     get_consensus = get_consensus
     get_chrom = get_chrom
     get_sample = get_sample
     get_consensus_matches = get_consensus_matches
-    compress = compress
-    compress_features = compress_features
-    compress_ms2 = compress_ms2
-    compress_chrom = compress_chrom
-    restore_features = restore_features
-    restore_chrom = restore_chrom
-    restore_ms2 = restore_ms2
-    decompress = decompress
-    fill_reset = fill_reset
-    align_reset = align_reset
-    set_source = set_source
-    sample_color = sample_color
-    sample_color_reset = sample_color_reset
-    name_replace = sample_name_replace
-    name_reset = sample_name_reset
+    get_consensus_matrix = get_consensus_matrix
+    get_gaps_matrix = get_gaps_matrix
+    get_gaps_stats = get_gaps_stats
+    get_orphans = get_orphans
+    
+    # === Data Selection and Filtering ===
     samples_select = samples_select
     samples_delete = samples_delete
     features_select = features_select
@@ -413,16 +405,67 @@ class Study:
     consensus_select = consensus_select
     consensus_filter = consensus_filter
     consensus_delete = consensus_delete
+    # Backward compatibility aliases
     filter_consensus = consensus_filter
     select_consensus = consensus_select
     filter_features = features_filter
     select_features = features_select
     consensus_find = merge
-    filter_features = features_filter
-
-    add_folder = add  # backward compatibility alias
-    add = add
-    add_sample = add_sample
+    
+    # === Sample Metadata and Styling ===
+    set_source = set_source
+    sample_color = sample_color
+    sample_color_reset = sample_color_reset
+    name_replace = sample_name_replace
+    name_reset = sample_name_reset
+    
+    # === Data Compression and Storage ===
+    compress = compress
+    compress_features = compress_features
+    compress_ms2 = compress_ms2
+    compress_chrom = compress_chrom
+    restore_features = restore_features
+    restore_chrom = restore_chrom
+    restore_ms2 = restore_ms2
+    decompress = decompress
+    
+    # === Reset Operations ===
+    fill_reset = fill_reset
+    align_reset = align_reset
+    
+    # === Plotting and Visualization ===
+    plot_alignment = plot_alignment
+    plot_chrom = plot_chrom
+    plot_consensus_2d = plot_consensus_2d
+    plot_consensus_stats = plot_consensus_stats
+    plot_pca = plot_pca
+    plot_samples_2d = plot_samples_2d
+    plot_bpc = plot_bpc
+    plot_rt_correction = plot_rt_correction
+    plot_tic = plot_tic
+    plot_eic = plot_eic
+    
+    # === Export Operations ===
+    export_mgf = export_mgf
+    export_mztab = export_mztab
+    export_xlsx = export_xlsx
+    export_parquet = export_parquet
+    
+    # === Identification and Library Matching ===
+    lib_load = lib_load
+    identify = identify
+    get_id = get_id
+    id_reset = id_reset
+    lib_reset = lib_reset
+    
+    # === Parameter Management ===
+    store_history = store_history
+    get_parameters = get_parameters
+    update_parameters = update_parameters
+    get_parameters_property = get_parameters_property
+    set_parameters_property = set_parameters_property
+    
+    # === Private/Internal Methods ===
     _add_samples_batch = _add_samples_batch
     _add_sample_optimized = _add_sample_optimized
     _add_sample_standard = _add_sample_standard
@@ -434,38 +477,20 @@ class Study:
     _get_feature_uids = _get_feature_uids
     _get_sample_uids = _get_sample_uids
     _ensure_features_df_schema_order = _ensure_features_df_schema_order
-    get_consensus_matrix = get_consensus_matrix
-    get_gaps_matrix = get_gaps_matrix
-    get_gaps_stats = get_gaps_stats
-    get_orphans = get_orphans
-    set_folder = set_folder
-    fill = fill
-    fill_chrom = fill  # Backward compatibility alias
     _process_sample_for_parallel_fill = _process_sample_for_parallel_fill
     _get_missing_consensus_sample_combinations = (
         _get_missing_consensus_sample_combinations
     )
     _load_consensusXML = _load_consensusXML
     load_features = load_features
-    sanitize = sanitize
     _save_consensusXML = _save_consensusXML
-    export_mgf = export_mgf
-    export_mztab = export_mztab
-    export_xlsx = export_xlsx
-    export_parquet = export_parquet
-    _get_mgf_df = _get_mgf_df  # New function for MGF data extraction
-    # Identification helpers
-    lib_load = lib_load
-    identify = identify
-    get_id = get_id
-    id_reset = id_reset
-    lib_reset = lib_reset
+    _get_mgf_df = _get_mgf_df
     _get_adducts = _get_adducts
     _calculate_formula_mass_shift = _calculate_formula_mass_shift
     _format_adduct_name = _format_adduct_name
     _parse_element_counts = _parse_element_counts
-
-    # defaults
+    
+    # === Default Parameters ===
     study_defaults = study_defaults
     align_defaults = align_defaults
     export_mgf_defaults = export_mgf_defaults
@@ -526,7 +551,17 @@ class Study:
             ):
                 sample_modules.append(module_name)
 
-        all_modules_to_reload = core_modules + sample_modules + study_modules
+        # Add lib submodules
+        lib_modules = []
+        lib_module_prefix = f"{base_modname}.lib."
+        for module_name in sys.modules:
+            if (
+                module_name.startswith(lib_module_prefix)
+                and module_name != current_module
+            ):
+                lib_modules.append(module_name)
+
+        all_modules_to_reload = core_modules + sample_modules + study_modules + lib_modules
 
         # Reload all discovered modules
         for full_module_name in all_modules_to_reload: