masster 0.4.4__py3-none-any.whl → 0.4.5__py3-none-any.whl

masster/study/id.py

@@ -3,14 +3,19 @@
 Identification helpers for Study: load a Lib and identify consensus features
 by matching m/z (and optionally RT).
 """
+
 from __future__ import annotations
 
-from typing import Optional
 
 import polars as pl
 
 
-def lib_load(study, lib_source, polarity: Optional[str] = None, adducts: Optional[list] = None):
+def lib_load(
+    study,
+    lib_source,
+    polarity: str | None = None,
+    adducts: list | None = None,
+):
     """Load a co    # Add compound and formula count columns
     if "consensus_uid" in result_df.columns:
         # Calculate counts per consensus_uid
@@ -31,7 +36,7 @@ def lib_load(study, lib_source, polarity: Optional[str] = None, adducts: Optiona
     """
     # Lazy import to avoid circular imports at module import time
     try:
-        from masster.lib.lib import Lib
+        from master.lib.lib import Lib
     except Exception:
         Lib = None
 
@@ -40,72 +45,93 @@ def lib_load(study, lib_source, polarity: Optional[str] = None, adducts: Optiona
 
     # Use study polarity if not explicitly provided
     if polarity is None:
-        study_polarity = getattr(study, 'polarity', 'positive')
+        study_polarity = getattr(study, "polarity", "positive")
         # Normalize polarity names
-        if study_polarity in ['pos', 'positive']:
-            polarity = 'positive'
-        elif study_polarity in ['neg', 'negative']:
-            polarity = 'negative'
+        if study_polarity in ["pos", "positive"]:
+            polarity = "positive"
+        elif study_polarity in ["neg", "negative"]:
+            polarity = "negative"
         else:
-            polarity = 'positive'  # Default fallback
+            polarity = "positive"  # Default fallback
 
     # Handle string input (CSV file path)
     if isinstance(lib_source, str):
         if Lib is None:
-            raise ImportError("Could not import masster.lib.lib.Lib - required for CSV loading")
-        
+            raise ImportError(
+                "Could not import master.lib.lib.Lib - required for CSV loading",
+            )
+
         lib_obj = Lib()
         lib_obj.import_csv(lib_source, polarity=polarity, adducts=adducts)
-        
+
     # Handle Lib instance
     elif Lib is not None and isinstance(lib_source, Lib):
         lib_obj = lib_source
-        
+
     # Handle other objects with lib_df attribute
     elif hasattr(lib_source, "lib_df"):
         lib_obj = lib_source
-        
+
     else:
-        raise TypeError("lib_source must be a CSV file path (str), a masster.lib.Lib instance, or have a 'lib_df' attribute")
+        raise TypeError(
+            "lib_source must be a CSV file path (str), a master.lib.Lib instance, or have a 'lib_df' attribute",
+        )
 
     # Ensure lib_df is populated
     lf = getattr(lib_obj, "lib_df", None)
-    if lf is None or (hasattr(lf, 'is_empty') and lf.is_empty()):
+    if lf is None or (hasattr(lf, "is_empty") and lf.is_empty()):
         raise ValueError("Library has no data populated in lib_df")
 
     # Filter by polarity to match study
     # Map polarity to charge signs
-    if polarity == 'positive':
+    if polarity == "positive":
         target_charges = [1, 2]  # positive charges
-    elif polarity == 'negative':
+    elif polarity == "negative":
         target_charges = [-1, -2]  # negative charges
     else:
         target_charges = [-2, -1, 1, 2]  # all charges
 
     # Filter library entries by charge sign (which corresponds to polarity)
     filtered_lf = lf.filter(pl.col("z").is_in(target_charges))
-    
+
     if filtered_lf.is_empty():
-        print(f"Warning: No library entries found for polarity '{polarity}'. Using all entries.")
+        print(
+            f"Warning: No library entries found for polarity '{polarity}'. Using all entries.",
+        )
         filtered_lf = lf
 
     # Store pointer and DataFrame on study
     study._lib = lib_obj
-    
+
     # Add to existing lib_df instead of replacing
-    if hasattr(study, 'lib_df') and study.lib_df is not None and not study.lib_df.is_empty():
+    if (
+        hasattr(study, "lib_df")
+        and study.lib_df is not None
+        and not study.lib_df.is_empty()
+    ):
         # Concatenate with existing data
         study.lib_df = pl.concat([study.lib_df, filtered_lf])
     else:
         # First time loading - create new
         try:
-            study.lib_df = filtered_lf.clone() if hasattr(filtered_lf, "clone") else pl.DataFrame(filtered_lf)
+            study.lib_df = (
+                filtered_lf.clone()
+                if hasattr(filtered_lf, "clone")
+                else pl.DataFrame(filtered_lf)
+            )
         except Exception:
-            study.lib_df = pl.from_pandas(filtered_lf) if hasattr(filtered_lf, "to_pandas") else pl.DataFrame(filtered_lf)
+            study.lib_df = (
+                pl.from_pandas(filtered_lf)
+                if hasattr(filtered_lf, "to_pandas")
+                else pl.DataFrame(filtered_lf)
+            )
 
     # Store this operation in history
-    if hasattr(study, 'store_history'):
-        study.store_history(["lib_load"], {"lib_source": str(lib_source), "polarity": polarity, "adducts": adducts})
+    if hasattr(study, "store_history"):
+        study.store_history(
+            ["lib_load"],
+            {"lib_source": str(lib_source), "polarity": polarity, "adducts": adducts},
+        )
 
 
 def identify(study, features=None, params=None, **kwargs):
@@ -121,7 +147,7 @@ def identify(study, features=None, params=None, **kwargs):
                  If None, identifies all consensus features.
         params: Optional identify_defaults instance with matching tolerances and scoring parameters.
                 If None, uses default parameters.
-        **kwargs: Individual parameter overrides (mz_tol, rt_tol, heteroatom_penalty, 
+        **kwargs: Individual parameter overrides (mz_tol, rt_tol, heteroatom_penalty,
                  multiple_formulas_penalty, multiple_compounds_penalty, heteroatoms)
 
     The resulting DataFrame is stored as study.id_df. Columns:
@@ -133,10 +159,10 @@ def identify(study, features=None, params=None, **kwargs):
     """
     # Import defaults class
     try:
-        from masster.study.defaults.identify_def import identify_defaults
+        from master.study.defaults.identify_def import identify_defaults
     except ImportError:
         identify_defaults = None
-    
+
     # Use provided params or create defaults
     if params is None:
         if identify_defaults is not None:
@@ -150,52 +176,66 @@ def identify(study, features=None, params=None, **kwargs):
                 multiple_formulas_penalty = 0.8
                 multiple_compounds_penalty = 0.8
                 heteroatoms = ["Cl", "Br", "F", "I"]
+
             params = FallbackParams()
-    
+
     # Override parameters with any provided kwargs
     if kwargs:
         for param_name, value in kwargs.items():
             if hasattr(params, param_name):
                 setattr(params, param_name, value)
-    
+
     # Get effective tolerances from params (now possibly overridden)
-    effective_mz_tol = getattr(params, 'mz_tol', 0.01)
-    effective_rt_tol = getattr(params, 'rt_tol', 2.0)
+    effective_mz_tol = getattr(params, "mz_tol", 0.01)
+    effective_rt_tol = getattr(params, "rt_tol", 2.0)
     # Get logger from study if available
-    logger = getattr(study, 'logger', None)
-    
+    logger = getattr(study, "logger", None)
+
     if logger:
-        logger.debug(f"Starting identification with mz_tolerance={effective_mz_tol}, rt_tolerance={effective_rt_tol}")
+        logger.debug(
+            f"Starting identification with mz_tolerance={effective_mz_tol}, rt_tolerance={effective_rt_tol}",
+        )
 
     # Determine which features to process
     target_uids = None
     if features is not None:
-        if hasattr(features, 'columns'):  # DataFrame-like
-            if 'consensus_uid' in features.columns:
-                target_uids = features['consensus_uid'].unique().to_list()
+        if hasattr(features, "columns"):  # DataFrame-like
+            if "consensus_uid" in features.columns:
+                target_uids = features["consensus_uid"].unique().to_list()
             else:
-                raise ValueError("features DataFrame must contain 'consensus_uid' column")
-        elif hasattr(features, '__iter__') and not isinstance(features, str):  # List-like
+                raise ValueError(
+                    "features DataFrame must contain 'consensus_uid' column",
+                )
+        elif hasattr(features, "__iter__") and not isinstance(
+            features,
+            str,
+        ):  # List-like
             target_uids = list(features)
         else:
-            raise ValueError("features must be a DataFrame with 'consensus_uid' column or a list of UIDs")
-        
+            raise ValueError(
+                "features must be a DataFrame with 'consensus_uid' column or a list of UIDs",
+            )
+
         if logger:
             logger.debug(f"Identifying {len(target_uids)} specified features")
 
     # Clear previous identification results for target features only
-    if hasattr(study, 'id_df') and not study.id_df.is_empty():
+    if hasattr(study, "id_df") and not study.id_df.is_empty():
         if target_uids is not None:
             # Keep results for features NOT being re-identified
-            study.id_df = study.id_df.filter(~pl.col("consensus_uid").is_in(target_uids))
+            study.id_df = study.id_df.filter(
+                ~pl.col("consensus_uid").is_in(target_uids),
+            )
             if logger:
-                logger.debug(f"Cleared previous identification results for {len(target_uids)} features")
+                logger.debug(
+                    f"Cleared previous identification results for {len(target_uids)} features",
+                )
         else:
             # Clear all results if no specific features specified
             study.id_df = pl.DataFrame()
             if logger:
                 logger.debug("Cleared all previous identification results")
-    elif not hasattr(study, 'id_df'):
+    elif not hasattr(study, "id_df"):
         study.id_df = pl.DataFrame()
         if logger:
             logger.debug("Initialized empty id_df")
@@ -214,20 +254,28 @@ def identify(study, features=None, params=None, **kwargs):
     # Filter consensus features if target_uids specified
     consensus_to_process = study.consensus_df
     if target_uids is not None:
-        consensus_to_process = study.consensus_df.filter(pl.col("consensus_uid").is_in(target_uids))
+        consensus_to_process = study.consensus_df.filter(
+            pl.col("consensus_uid").is_in(target_uids),
+        )
         if consensus_to_process.is_empty():
             if logger:
-                logger.warning("No consensus features found matching specified features")
+                logger.warning(
+                    "No consensus features found matching specified features",
+                )
             return
 
     consensus_count = len(consensus_to_process)
     lib_count = len(study.lib_df)
-    
+
     if logger:
         if target_uids is not None:
-            logger.debug(f"Identifying {consensus_count} specified consensus features against {lib_count} library entries")
+            logger.debug(
+                f"Identifying {consensus_count} specified consensus features against {lib_count} library entries",
+            )
         else:
-            logger.debug(f"Identifying {consensus_count} consensus features against {lib_count} library entries")
+            logger.debug(
+                f"Identifying {consensus_count} consensus features against {lib_count} library entries",
+            )
 
     # Get adduct probabilities
     adducts_df = study._get_adducts()
@@ -235,7 +283,7 @@ def identify(study, features=None, params=None, **kwargs):
     if not adducts_df.is_empty():
         for row in adducts_df.iter_rows(named=True):
             adduct_prob_map[row.get("name")] = row.get("probability", 1.0)
-    
+
     results = []
     features_with_matches = 0
     total_matches = 0
@@ -247,7 +295,7 @@ def identify(study, features=None, params=None, **kwargs):
         cons_mz = cons.get("mz")
         cons_rt = cons.get("rt")
         cons_uid = cons.get("consensus_uid")
-        
+
         if cons_mz is None:
             if logger:
                 logger.debug(f"Skipping consensus feature {cons_uid} - no m/z value")
@@ -255,7 +303,8 @@ def identify(study, features=None, params=None, **kwargs):
 
         # Filter lib by mz window
         matches = study.lib_df.filter(
-            (pl.col("mz") >= cons_mz - effective_mz_tol) & (pl.col("mz") <= cons_mz + effective_mz_tol)
+            (pl.col("mz") >= cons_mz - effective_mz_tol)
+            & (pl.col("mz") <= cons_mz + effective_mz_tol),
         )
 
         initial_matches = len(matches)
@@ -263,15 +312,21 @@ def identify(study, features=None, params=None, **kwargs):
         # If rt_tol provided and consensus RT present, prefer rt-filtered hits
         if effective_rt_tol is not None and cons_rt is not None:
             rt_matches = matches.filter(
-                pl.col("rt").is_not_null() & (pl.col("rt") >= cons_rt - effective_rt_tol) & (pl.col("rt") <= cons_rt + effective_rt_tol)
+                pl.col("rt").is_not_null()
+                & (pl.col("rt") >= cons_rt - effective_rt_tol)
+                & (pl.col("rt") <= cons_rt + effective_rt_tol),
             )
             if not rt_matches.is_empty():
                 matches = rt_matches
                 if logger:
-                    logger.debug(f"Consensus {cons_uid}: {initial_matches} m/z matches, {len(matches)} after RT filter")
+                    logger.debug(
+                        f"Consensus {cons_uid}: {initial_matches} m/z matches, {len(matches)} after RT filter",
+                    )
             else:
                 if logger:
-                    logger.debug(f"Consensus {cons_uid}: {initial_matches} m/z matches, 0 after RT filter - using m/z matches only")
+                    logger.debug(
+                        f"Consensus {cons_uid}: {initial_matches} m/z matches, 0 after RT filter - using m/z matches only",
+                    )
 
         # Apply scoring-based filtering system
         if not matches.is_empty():
@@ -283,19 +338,25 @@ def identify(study, features=None, params=None, **kwargs):
             features_with_matches += 1
             feature_match_count = len(filtered_matches)
             total_matches += feature_match_count
-            
+
             if logger:
-                logger.debug(f"Consensus {cons_uid} (mz={cons_mz:.5f}): {feature_match_count} library matches")
+                logger.debug(
+                    f"Consensus {cons_uid} (mz={cons_mz:.5f}): {feature_match_count} library matches",
+                )
 
         for m in filtered_matches.iter_rows(named=True):
             mz_delta = abs(cons_mz - m.get("mz")) if m.get("mz") is not None else None
             lib_rt = m.get("rt")
-            rt_delta = abs(cons_rt - lib_rt) if (cons_rt is not None and lib_rt is not None) else None
-            
+            rt_delta = (
+                abs(cons_rt - lib_rt)
+                if (cons_rt is not None and lib_rt is not None)
+                else None
+            )
+
             # Get adduct probability from _get_adducts() results
             adduct = m.get("adduct")
             score = adduct_prob_map.get(adduct, 1.0) if adduct else 1.0
-            
+
             results.append(
                 {
                     "consensus_uid": cons.get("consensus_uid"),
@@ -304,51 +365,60 @@ def identify(study, features=None, params=None, **kwargs):
                     "rt_delta": rt_delta,
                     "matcher": "ms1",
                     "score": score,
-                }
+                },
             )
 
     # Merge new results with existing results
     new_results_df = pl.DataFrame(results) if results else pl.DataFrame()
-    
+
     if not new_results_df.is_empty():
-        if hasattr(study, 'id_df') and not study.id_df.is_empty():
+        if hasattr(study, "id_df") and not study.id_df.is_empty():
             # Concatenate new results with existing results
             study.id_df = pl.concat([study.id_df, new_results_df])
         else:
             # First results
             study.id_df = new_results_df
-    
+
     # Apply scoring adjustments based on compound and formula counts
-    if not study.id_df.is_empty() and hasattr(study, 'lib_df') and not study.lib_df.is_empty():
+    if (
+        not study.id_df.is_empty()
+        and hasattr(study, "lib_df")
+        and not study.lib_df.is_empty()
+    ):
         # Join with lib_df to get compound and formula information
         id_with_lib = study.id_df.join(
             study.lib_df.select(["lib_uid", "cmpd_uid", "formula"]),
             on="lib_uid",
-            how="left"
+            how="left",
         )
-        
+
         # Calculate counts per consensus_uid
-        count_stats = id_with_lib.group_by("consensus_uid").agg([
-            pl.col("cmpd_uid").n_unique().alias("num_cmpds"),
-            pl.col("formula").filter(pl.col("formula").is_not_null()).n_unique().alias("num_formulas")
-        ])
-        
+        count_stats = id_with_lib.group_by("consensus_uid").agg(
+            [
+                pl.col("cmpd_uid").n_unique().alias("num_cmpds"),
+                pl.col("formula")
+                .filter(pl.col("formula").is_not_null())
+                .n_unique()
+                .alias("num_formulas"),
+            ],
+        )
+
         # Join counts back to id_df
         id_with_counts = study.id_df.join(count_stats, on="consensus_uid", how="left")
-        
+
         # Join with lib_df again to get formula information for heteroatom penalty
         id_with_formula = id_with_counts.join(
             study.lib_df.select(["lib_uid", "formula"]),
             on="lib_uid",
-            how="left"
+            how="left",
         )
-        
+
         # Apply scoring penalties
-        heteroatoms = getattr(params, 'heteroatoms', ['Cl', 'Br', 'F', 'I'])
-        heteroatom_penalty = getattr(params, 'heteroatom_penalty', 0.7)
-        formulas_penalty = getattr(params, 'multiple_formulas_penalty', 0.8)
-        compounds_penalty = getattr(params, 'multiple_compounds_penalty', 0.8)
-        
+        heteroatoms = getattr(params, "heteroatoms", ["Cl", "Br", "F", "I"])
+        heteroatom_penalty = getattr(params, "heteroatom_penalty", 0.7)
+        formulas_penalty = getattr(params, "multiple_formulas_penalty", 0.8)
+        compounds_penalty = getattr(params, "multiple_compounds_penalty", 0.8)
+
         # Build heteroatom condition
         heteroatom_condition = None
         for atom in heteroatoms:
@@ -357,76 +427,104 @@ def identify(study, features=None, params=None, **kwargs):
                 heteroatom_condition = atom_condition
             else:
                 heteroatom_condition = heteroatom_condition | atom_condition
-        
+
         # Apply penalties
-        study.id_df = id_with_formula.with_columns([
-            # Heteroatom penalty: if formula contains specified heteroatoms, apply penalty
-            pl.when(
-                pl.col("formula").is_not_null() & heteroatom_condition
+        study.id_df = (
+            id_with_formula.with_columns(
+                [
+                    # Heteroatom penalty: if formula contains specified heteroatoms, apply penalty
+                    pl.when(
+                        pl.col("formula").is_not_null() & heteroatom_condition,
+                    )
+                    .then(pl.col("score") * heteroatom_penalty)
+                    .otherwise(pl.col("score"))
+                    .alias("score_temp0"),
+                ],
+            )
+            .with_columns(
+                [
+                    # If num_formulas > 1, apply multiple formulas penalty
+                    pl.when(pl.col("num_formulas") > 1)
+                    .then(pl.col("score_temp0") * formulas_penalty)
+                    .otherwise(pl.col("score_temp0"))
+                    .alias("score_temp1"),
+                ],
             )
-            .then(pl.col("score") * heteroatom_penalty)
-            .otherwise(pl.col("score"))
-            .alias("score_temp0")
-        ]).with_columns([
-            # If num_formulas > 1, apply multiple formulas penalty
-            pl.when(pl.col("num_formulas") > 1)
-            .then(pl.col("score_temp0") * formulas_penalty)
-            .otherwise(pl.col("score_temp0"))
-            .alias("score_temp1")
-        ]).with_columns([
-            # If num_cmpds > 1, apply multiple compounds penalty
-            pl.when(pl.col("num_cmpds") > 1)
-            .then(pl.col("score_temp1") * compounds_penalty) 
-            .otherwise(pl.col("score_temp1"))
-            .round(4)  # Round to 4 decimal places
-            .alias("score")
-        ]).select([
-            "consensus_uid", "lib_uid", "mz_delta", "rt_delta", "matcher", "score"
-        ])
-    
+            .with_columns(
+                [
+                    # If num_cmpds > 1, apply multiple compounds penalty
+                    pl.when(pl.col("num_cmpds") > 1)
+                    .then(pl.col("score_temp1") * compounds_penalty)
+                    .otherwise(pl.col("score_temp1"))
+                    .round(4)  # Round to 4 decimal places
+                    .alias("score"),
+                ],
+            )
+            .select(
+                [
+                    "consensus_uid",
+                    "lib_uid",
+                    "mz_delta",
+                    "rt_delta",
+                    "matcher",
+                    "score",
+                ],
+            )
+        )
+
     # Store this operation in history
-    if hasattr(study, 'store_history'):
+    if hasattr(study, "store_history"):
         history_params = {"mz_tol": effective_mz_tol, "rt_tol": effective_rt_tol}
         if features is not None:
             history_params["features"] = target_uids
-        if params is not None and hasattr(params, 'to_dict'):
+        if params is not None and hasattr(params, "to_dict"):
             history_params["params"] = params.to_dict()
         if kwargs:
             history_params["kwargs"] = kwargs
         study.store_history(["identify"], history_params)
-    
+
     if logger:
         if rt_filtered_compounds > 0:
-            logger.debug(f"RT consistency filtering applied to {rt_filtered_compounds} compound groups")
-        
+            logger.debug(
+                f"RT consistency filtering applied to {rt_filtered_compounds} compound groups",
+            )
+
         if multiply_charged_filtered > 0:
-            logger.debug(f"Excluded {multiply_charged_filtered} multiply charged adducts (no [M+H]+ or [M-H]- coeluting)")
-        
-        logger.info(f"Identification completed: {features_with_matches}/{consensus_count} features matched, {total_matches} total identifications")
-        
-        
+            logger.debug(
+                f"Excluded {multiply_charged_filtered} multiply charged adducts (no [M+H]+ or [M-H]- coeluting)",
+            )
+
+        logger.info(
+            f"Identification completed: {features_with_matches}/{consensus_count} features matched, {total_matches} total identifications",
+        )
+
         if total_matches > 0:
             # Calculate some statistics
             mz_deltas = [r["mz_delta"] for r in results if r["mz_delta"] is not None]
             rt_deltas = [r["rt_delta"] for r in results if r["rt_delta"] is not None]
             scores = [r["score"] for r in results if r["score"] is not None]
-            
+
             if mz_deltas:
                 avg_mz_delta = sum(mz_deltas) / len(mz_deltas)
                 max_mz_delta = max(mz_deltas)
-                logger.debug(f"m/z accuracy: average Δ={avg_mz_delta:.5f} Da, max Δ={max_mz_delta:.5f} Da")
-            
+                logger.debug(
+                    f"m/z accuracy: average Δ={avg_mz_delta:.5f} Da, max Δ={max_mz_delta:.5f} Da",
+                )
+
             if rt_deltas:
                 avg_rt_delta = sum(rt_deltas) / len(rt_deltas)
                 max_rt_delta = max(rt_deltas)
-                logger.debug(f"RT accuracy: average Δ={avg_rt_delta:.2f} min, max Δ={max_rt_delta:.2f} min")
-            
+                logger.debug(
+                    f"RT accuracy: average Δ={avg_rt_delta:.2f} min, max Δ={max_rt_delta:.2f} min",
+                )
+
             if scores:
                 avg_score = sum(scores) / len(scores)
                 min_score = min(scores)
                 max_score = max(scores)
-                logger.debug(f"Adduct probability scores: average={avg_score:.3f}, min={min_score:.3f}, max={max_score:.3f}")
-    
+                logger.debug(
+                    f"Adduct probability scores: average={avg_score:.3f}, min={min_score:.3f}, max={max_score:.3f}",
+                )
 
 
 def get_id(study, features=None) -> pl.DataFrame:
@@ -443,7 +541,7 @@ def get_id(study, features=None) -> pl.DataFrame:
     Returns:
         Polars DataFrame with columns:
         - consensus_uid
-        - lib_uid  
+        - lib_uid
         - mz (consensus feature m/z)
         - rt (consensus feature RT)
         - name (compound name from library)
@@ -459,7 +557,9 @@ def get_id(study, features=None) -> pl.DataFrame:
     """
     # Validate inputs
     if getattr(study, "id_df", None) is None or study.id_df.is_empty():
-        raise ValueError("Identification results (study.id_df) are empty; call identify() first")
+        raise ValueError(
+            "Identification results (study.id_df) are empty; call identify() first",
+        )
 
     if getattr(study, "lib_df", None) is None or study.lib_df.is_empty():
         raise ValueError("Library (study.lib_df) is empty; call lib_load() first")
@@ -472,35 +572,52 @@ def get_id(study, features=None) -> pl.DataFrame:
 
     # Filter by features if provided
     if features is not None:
-        if hasattr(features, 'columns'):  # DataFrame-like
-            if 'consensus_uid' in features.columns:
-                uids = features['consensus_uid'].unique().to_list()
+        if hasattr(features, "columns"):  # DataFrame-like
+            if "consensus_uid" in features.columns:
+                uids = features["consensus_uid"].unique().to_list()
             else:
-                raise ValueError("features DataFrame must contain 'consensus_uid' column")
-        elif hasattr(features, '__iter__') and not isinstance(features, str):  # List-like
+                raise ValueError(
+                    "features DataFrame must contain 'consensus_uid' column",
+                )
+        elif hasattr(features, "__iter__") and not isinstance(
+            features,
+            str,
+        ):  # List-like
             uids = list(features)
         else:
-            raise ValueError("features must be a DataFrame with 'consensus_uid' column or a list of UIDs")
-        
+            raise ValueError(
+                "features must be a DataFrame with 'consensus_uid' column or a list of UIDs",
+            )
+
         result_df = result_df.filter(pl.col("consensus_uid").is_in(uids))
-        
+
         if result_df.is_empty():
             return pl.DataFrame()
 
     # Join with consensus_df to get consensus feature m/z and RT
     consensus_cols = ["consensus_uid", "mz", "rt"]
     # Only select columns that exist in consensus_df
-    available_consensus_cols = [col for col in consensus_cols if col in study.consensus_df.columns]
-    
+    available_consensus_cols = [
+        col for col in consensus_cols if col in study.consensus_df.columns
+    ]
+
     result_df = result_df.join(
         study.consensus_df.select(available_consensus_cols),
         on="consensus_uid",
         how="left",
-        suffix="_consensus"
+        suffix="_consensus",
     )
 
     # Join with lib_df to get library information
-    lib_cols = ["lib_uid", "name", "formula", "adduct", "smiles", "cmpd_uid", "inchikey"]
+    lib_cols = [
+        "lib_uid",
+        "name",
+        "formula",
+        "adduct",
+        "smiles",
+        "cmpd_uid",
+        "inchikey",
+    ]
     # Add optional columns if they exist
     optional_lib_cols = ["inchi", "db_id", "db"]
     for col in optional_lib_cols:
@@ -509,19 +626,19 @@ def get_id(study, features=None) -> pl.DataFrame:
 
     # Only select columns that exist in lib_df
     available_lib_cols = [col for col in lib_cols if col in study.lib_df.columns]
-    
+
     result_df = result_df.join(
         study.lib_df.select(available_lib_cols),
-        on="lib_uid", 
+        on="lib_uid",
         how="left",
-        suffix="_lib"
+        suffix="_lib",
     )
 
     # Reorder columns for better readability
     column_order = [
         "consensus_uid",
         "cmpd_uid" if "cmpd_uid" in result_df.columns else None,
-        "lib_uid", 
+        "lib_uid",
         "name" if "name" in result_df.columns else None,
         "formula" if "formula" in result_df.columns else None,
         "adduct" if "adduct" in result_df.columns else None,
@@ -532,34 +649,57 @@ def get_id(study, features=None) -> pl.DataFrame:
         "matcher" if "matcher" in result_df.columns else None,
         "score" if "score" in result_df.columns else None,
         "smiles" if "smiles" in result_df.columns else None,
-        "inchikey" if "inchikey" in result_df.columns else None
+        "inchikey" if "inchikey" in result_df.columns else None,
     ]
-    
+
     # Add any remaining columns
     remaining_cols = [col for col in result_df.columns if col not in column_order]
     column_order.extend(remaining_cols)
-    
+
     # Filter out None values and select existing columns
-    final_column_order = [col for col in column_order if col is not None and col in result_df.columns]
-    
+    final_column_order = [
+        col for col in column_order if col is not None and col in result_df.columns
+    ]
+
     result_df = result_df.select(final_column_order)
-    
+
     # Add compound and formula count columns
     if "consensus_uid" in result_df.columns:
         # Calculate counts per consensus_uid
-        count_stats = result_df.group_by("consensus_uid").agg([
-            pl.col("cmpd_uid").n_unique().alias("num_cmpds") if "cmpd_uid" in result_df.columns else pl.lit(None).alias("num_cmpds"),
-            pl.col("formula").filter(pl.col("formula").is_not_null()).n_unique().alias("num_formulas") if "formula" in result_df.columns else pl.lit(None).alias("num_formulas")
-        ])
-        
+        count_stats = result_df.group_by("consensus_uid").agg(
+            [
+                pl.col("cmpd_uid").n_unique().alias("num_cmpds")
+                if "cmpd_uid" in result_df.columns
+                else pl.lit(None).alias("num_cmpds"),
+                pl.col("formula")
+                .filter(pl.col("formula").is_not_null())
+                .n_unique()
+                .alias("num_formulas")
+                if "formula" in result_df.columns
+                else pl.lit(None).alias("num_formulas"),
+            ],
+        )
+
         # Join the counts back to the main dataframe
         result_df = result_df.join(count_stats, on="consensus_uid", how="left")
-        
+
         # Reorder columns to put count columns in the right position
         final_columns = []
         for col in result_df.columns:
-            if col in ["consensus_uid", "cmpd_uid", "lib_uid", "name", "formula", "adduct", 
-                      "mz", "mz_delta", "rt", "rt_delta", "matcher", "score"]:
+            if col in [
+                "consensus_uid",
+                "cmpd_uid",
+                "lib_uid",
+                "name",
+                "formula",
+                "adduct",
+                "mz",
+                "mz_delta",
+                "rt",
+                "rt_delta",
+                "matcher",
+                "score",
+            ]:
                 final_columns.append(col)
         # Add count columns
         if "num_cmpds" in result_df.columns:
@@ -570,143 +710,160 @@ def get_id(study, features=None) -> pl.DataFrame:
         for col in result_df.columns:
             if col not in final_columns:
                 final_columns.append(col)
-        
+
         result_df = result_df.select(final_columns)
-        
+
         # Apply filtering logic (scores are already final from identify())
         if "consensus_uid" in result_df.columns and len(result_df) > 0:
             # (v) Rank by score, assume that highest score has the correct rt
             # (vi) Remove all lower-scoring ids with a different rt (group by cmpd_uid)
             # (vii) Remove multiply charged ids if not in line with [M+H]+ or [M-H]- (group by cmpd_uid)
-            
+
             # Group by cmpd_uid and apply filtering logic
             if "cmpd_uid" in result_df.columns:
                 filtered_dfs = []
                 for cmpd_uid, group_df in result_df.group_by("cmpd_uid"):
                     # Sort by score descending to get highest score first
                     group_df = group_df.sort("score", descending=True)
-                    
+
                     if len(group_df) == 0:
                         continue
-                        
+
                     # Get the highest scoring entry's RT as reference
-                    reference_rt = group_df["rt"][0] if "rt" in group_df.columns and group_df["rt"][0] is not None else None
-                    
+                    reference_rt = (
+                        group_df["rt"][0]
+                        if "rt" in group_df.columns and group_df["rt"][0] is not None
+                        else None
+                    )
+
                     # Filter entries: keep those with same RT as highest scoring entry
                     if reference_rt is not None and "rt" in group_df.columns:
                         # Keep entries with the same RT or null RT
                         rt_filtered = group_df.filter(
-                            (pl.col("rt") == reference_rt) | pl.col("rt").is_null()
+                            (pl.col("rt") == reference_rt) | pl.col("rt").is_null(),
                         )
                     else:
                         # No reference RT, keep all
                         rt_filtered = group_df
-                    
+
                     # Check multiply charged constraint
-                    if "z" in rt_filtered.columns and "adduct" in rt_filtered.columns and len(rt_filtered) > 0:
+                    if (
+                        "z" in rt_filtered.columns
+                        and "adduct" in rt_filtered.columns
+                        and len(rt_filtered) > 0
+                    ):
                         # Check if there are multiply charged adducts
-                        multiply_charged = rt_filtered.filter((pl.col("z") > 1) | (pl.col("z") < -1))
-                        singly_charged = rt_filtered.filter((pl.col("z") == 1) | (pl.col("z") == -1))
-                        
+                        multiply_charged = rt_filtered.filter(
+                            (pl.col("z") > 1) | (pl.col("z") < -1),
+                        )
+                        singly_charged = rt_filtered.filter(
+                            (pl.col("z") == 1) | (pl.col("z") == -1),
+                        )
+
                         if not multiply_charged.is_empty():
                             # Check if [M+H]+ or [M-H]- are present
                             reference_adducts = ["[M+H]+", "[M-H]-"]
-                            has_reference = any(singly_charged.filter(pl.col("adduct").is_in(reference_adducts)).height > 0)
-                            
+                            has_reference = any(
+                                singly_charged.filter(
+                                    pl.col("adduct").is_in(reference_adducts),
+                                ).height
+                                > 0,
+                            )
+
                             if not has_reference:
                                 # Remove multiply charged adducts
                                 rt_filtered = singly_charged
-                    
+
                     if len(rt_filtered) > 0:
                         filtered_dfs.append(rt_filtered)
-                
+
                 if filtered_dfs:
                     result_df = pl.concat(filtered_dfs)
                 else:
                     result_df = pl.DataFrame()
-    
+
     # Sort by cmpd_uid if available
     if "cmpd_uid" in result_df.columns:
         result_df = result_df.sort("cmpd_uid")
-    
+
     return result_df
 
 
 def id_reset(study):
     """Reset identification data and remove from history.
-    
+
     Removes:
     - study.id_df (identification results DataFrame)
     - 'identify' from study.history
-    
+
     Args:
         study: Study instance to reset
     """
     # Get logger from study if available
-    logger = getattr(study, 'logger', None)
-    
+    logger = getattr(study, "logger", None)
+
     # Remove id_df
-    if hasattr(study, 'id_df'):
+    if hasattr(study, "id_df"):
         if logger:
             logger.debug("Removing id_df")
-        delattr(study, 'id_df')
-    
+        delattr(study, "id_df")
+
     # Remove identify from history
-    if hasattr(study, 'history') and 'identify' in study.history:
+    if hasattr(study, "history") and "identify" in study.history:
         if logger:
             logger.debug("Removing 'identify' from history")
-        del study.history['identify']
-    
+        del study.history["identify"]
+
     if logger:
         logger.info("Identification data reset completed")
 
 
 def lib_reset(study):
     """Reset library and identification data and remove from history.
-    
+
     Removes:
-    - study.id_df (identification results DataFrame) 
+    - study.id_df (identification results DataFrame)
     - study.lib_df (library DataFrame)
     - study._lib (library object reference)
     - 'identify' from study.history
     - 'lib_load' from study.history (if exists)
-    
+
     Args:
         study: Study instance to reset
     """
     # Get logger from study if available
-    logger = getattr(study, 'logger', None)
-    
+    logger = getattr(study, "logger", None)
+
     # Remove id_df
-    if hasattr(study, 'id_df'):
+    if hasattr(study, "id_df"):
         if logger:
             logger.debug("Removing id_df")
-        delattr(study, 'id_df')
-    
-    # Remove lib_df  
-    if hasattr(study, 'lib_df'):
+        delattr(study, "id_df")
+
+    # Remove lib_df
+    if hasattr(study, "lib_df"):
         if logger:
             logger.debug("Removing lib_df")
-        delattr(study, 'lib_df')
-    
+        delattr(study, "lib_df")
+
     # Remove lib object reference
-    if hasattr(study, '_lib'):
+    if hasattr(study, "_lib"):
         if logger:
             logger.debug("Removing _lib reference")
-        delattr(study, '_lib')
-    
+        delattr(study, "_lib")
+
     # Remove from history
-    if hasattr(study, 'history'):
-        if 'identify' in study.history:
+    if hasattr(study, "history"):
+        if "identify" in study.history:
             if logger:
                 logger.debug("Removing 'identify' from history")
-            del study.history['identify']
-        
-        if 'lib_load' in study.history:
+            del study.history["identify"]
+
+        if "lib_load" in study.history:
             if logger:
                 logger.debug("Removing 'lib_load' from history")
-            del study.history['lib_load']
-    
+            del study.history["lib_load"]
+
     if logger:
         logger.info("Library and identification data reset completed")
 
@@ -714,11 +871,11 @@ def lib_reset(study):
 def _get_adducts(self, adducts_list: list = None, **kwargs):
     """
     Generate comprehensive adduct specifications for study-level adduct filtering.
-    
+
     This method creates a DataFrame of adduct combinations that will be used to filter
     and score adducts at the study level. Similar to sample._get_adducts() but uses
     study-level parameters and constraints.
-    
+
     Parameters
     ----------
     adducts_list : List[str], optional
@@ -727,10 +884,10 @@ def _get_adducts(self, adducts_list: list = None, **kwargs):
     **kwargs : dict
         Override parameters, including:
         - charge_min: Minimum charge to consider (default 1)
-        - charge_max: Maximum charge to consider (default 3)  
+        - charge_max: Maximum charge to consider (default 3)
         - max_combinations: Maximum number of adduct components to combine (default 3)
         - min_probability: Minimum probability threshold (default from study parameters)
-        
+
     Returns
     -------
     pl.DataFrame
@@ -742,270 +899,302 @@ def _get_adducts(self, adducts_list: list = None, **kwargs):
         - complexity: Number of adduct components (1-3)
     """
     # Import required modules
-    from collections import Counter
-    from itertools import combinations
-    import numpy as np
-    
+
     # Use provided adducts list or get from study parameters
     if adducts_list is None:
-        adducts_list = self.parameters.adducts if hasattr(self.parameters, 'adducts') and self.parameters.adducts else []
-        
+        adducts_list = (
+            self.parameters.adducts
+            if hasattr(self.parameters, "adducts") and self.parameters.adducts
+            else []
+        )
+
     # Get parameters with study-specific defaults
-    charge_min = kwargs.get('charge_min', -3)  # Allow negative charges
-    charge_max = kwargs.get('charge_max', 3)   # Study uses up to charge ±3
-    max_combinations = kwargs.get('max_combinations', 3)  # Up to 3 combinations
-    min_probability = kwargs.get('min_probability', getattr(self.parameters, 'adduct_min_probability', 0.04))
-    
+    charge_min = kwargs.get("charge_min", -3)  # Allow negative charges
+    charge_max = kwargs.get("charge_max", 3)  # Study uses up to charge ±3
+    max_combinations = kwargs.get("max_combinations", 3)  # Up to 3 combinations
+    min_probability = kwargs.get(
+        "min_probability",
+        getattr(self.parameters, "adduct_min_probability", 0.04),
+    )
+
     # Parse base adduct specifications
     base_specs = []
-    
+
     for adduct_str in adducts_list:
-        if not isinstance(adduct_str, str) or ':' not in adduct_str:
+        if not isinstance(adduct_str, str) or ":" not in adduct_str:
             continue
-            
+
         try:
-            parts = adduct_str.split(':')
+            parts = adduct_str.split(":")
             if len(parts) != 3:
                 continue
-                
+
             formula_part = parts[0]
-            charge = int(parts[1]) 
+            charge = int(parts[1])
             probability = float(parts[2])
-            
+
             # Calculate mass shift from formula
             mass_shift = self._calculate_formula_mass_shift(formula_part)
-            
-            base_specs.append({
-                'formula': formula_part,
-                'charge': charge,
-                'mass_shift': mass_shift,
-                'probability': probability,
-                'raw_string': adduct_str
-            })
-            
+
+            base_specs.append(
+                {
+                    "formula": formula_part,
+                    "charge": charge,
+                    "mass_shift": mass_shift,
+                    "probability": probability,
+                    "raw_string": adduct_str,
+                },
+            )
+
         except (ValueError, IndexError):
             continue
-    
+
     if not base_specs:
         # Return empty DataFrame with correct schema
-        return pl.DataFrame({
-            'name': [],
-            'charge': [],
-            'mass_shift': [],
-            'probability': [],
-            'complexity': []
-        })
-    
+        return pl.DataFrame(
+            {
+                "name": [],
+                "charge": [],
+                "mass_shift": [],
+                "probability": [],
+                "complexity": [],
+            },
+        )
+
     # Generate all valid combinations
     combinations_list = []
-    
+
     # Separate specs by charge type
-    positive_specs = [spec for spec in base_specs if spec['charge'] > 0]
-    negative_specs = [spec for spec in base_specs if spec['charge'] < 0]
-    neutral_specs = [spec for spec in base_specs if spec['charge'] == 0]
-    
+    positive_specs = [spec for spec in base_specs if spec["charge"] > 0]
+    negative_specs = [spec for spec in base_specs if spec["charge"] < 0]
+    neutral_specs = [spec for spec in base_specs if spec["charge"] == 0]
+
     # 1. Single adducts (filter out neutral adducts with charge == 0)
     for spec in base_specs:
-        if charge_min <= spec['charge'] <= charge_max and spec['charge'] != 0:
+        if charge_min <= spec["charge"] <= charge_max and spec["charge"] != 0:
             formatted_name = self._format_adduct_name([spec])
-            combinations_list.append({
-                'components': [spec],
-                'formatted_name': formatted_name,
-                'total_mass_shift': spec['mass_shift'],
-                'total_charge': spec['charge'],
-                'combined_probability': spec['probability'],
-                'complexity': 1
-            })
-    
+            combinations_list.append(
+                {
+                    "components": [spec],
+                    "formatted_name": formatted_name,
+                    "total_mass_shift": spec["mass_shift"],
+                    "total_charge": spec["charge"],
+                    "combined_probability": spec["probability"],
+                    "complexity": 1,
+                },
+            )
+
     # 2. Generate multiply charged versions (2H+, 3H+, etc.) - already excludes charge==0
     for spec in positive_specs + negative_specs:
-        base_charge = spec['charge']
+        base_charge = spec["charge"]
         for multiplier in range(2, min(max_combinations + 1, 4)):  # Up to 3x multiplier
             total_charge = base_charge * multiplier
             if charge_min <= total_charge <= charge_max and total_charge != 0:
                 components = [spec] * multiplier
                 formatted_name = self._format_adduct_name(components)
-                
-                combinations_list.append({
-                    'components': components,
-                    'formatted_name': formatted_name,
-                    'total_mass_shift': spec['mass_shift'] * multiplier,
-                    'total_charge': total_charge,
-                    'combined_probability': spec['probability'] ** multiplier,
-                    'complexity': multiplier
-                })
-    
+
+                combinations_list.append(
+                    {
+                        "components": components,
+                        "formatted_name": formatted_name,
+                        "total_mass_shift": spec["mass_shift"] * multiplier,
+                        "total_charge": total_charge,
+                        "combined_probability": spec["probability"] ** multiplier,
+                        "complexity": multiplier,
+                    },
+                )
+
     # 3. Mixed combinations (2-component) - limited for study level, filter out charge==0
     if max_combinations >= 2:
         # Positive + Neutral (1 neutral loss only) - but exclude if total charge == 0
         for pos_spec in positive_specs[:2]:  # Limit to first 2 positive specs
             for neut_spec in neutral_specs[:1]:  # Only 1 neutral loss
-                total_charge = pos_spec['charge'] + neut_spec['charge']
+                total_charge = pos_spec["charge"] + neut_spec["charge"]
                 if charge_min <= total_charge <= charge_max and total_charge != 0:
                     components = [pos_spec, neut_spec]
                     formatted_name = self._format_adduct_name(components)
-                    combinations_list.append({
-                        'components': components,
-                        'formatted_name': formatted_name,
-                        'total_mass_shift': pos_spec['mass_shift'] + neut_spec['mass_shift'],
-                        'total_charge': total_charge,
-                        'combined_probability': pos_spec['probability'] * neut_spec['probability'],
-                        'complexity': 2
-                    })
-    
+                    combinations_list.append(
+                        {
+                            "components": components,
+                            "formatted_name": formatted_name,
+                            "total_mass_shift": pos_spec["mass_shift"]
+                            + neut_spec["mass_shift"],
+                            "total_charge": total_charge,
+                            "combined_probability": pos_spec["probability"]
+                            * neut_spec["probability"],
+                            "complexity": 2,
+                        },
+                    )
+
     # Convert to polars DataFrame
     if combinations_list:
-        combinations_list.sort(key=lambda x: (-x['combined_probability'], x['complexity']))
-        
-        adducts_df = pl.DataFrame([
-            {
-                'name': combo['formatted_name'],
-                'charge': combo['total_charge'], 
-                'mass_shift': combo['total_mass_shift'],
-                'probability': combo['combined_probability'],
-                'complexity': combo['complexity']
-            }
-            for combo in combinations_list
-        ])
-        
+        combinations_list.sort(
+            key=lambda x: (-x["combined_probability"], x["complexity"]),
+        )
+
+        adducts_df = pl.DataFrame(
+            [
+                {
+                    "name": combo["formatted_name"],
+                    "charge": combo["total_charge"],
+                    "mass_shift": combo["total_mass_shift"],
+                    "probability": combo["combined_probability"],
+                    "complexity": combo["complexity"],
+                }
+                for combo in combinations_list
+            ],
+        )
+
         # Filter by minimum probability threshold
         if min_probability > 0.0:
             adducts_before_filter = len(adducts_df)
             adducts_df = adducts_df.filter(pl.col("probability") >= min_probability)
             adducts_after_filter = len(adducts_df)
-            
-            self.logger.debug(f"Study adducts: generated {adducts_before_filter}, filtered to {adducts_after_filter} (min_prob={min_probability})")
-            
+
+            self.logger.debug(
+                f"Study adducts: generated {adducts_before_filter}, filtered to {adducts_after_filter} (min_prob={min_probability})",
+            )
+
     else:
         # Return empty DataFrame with correct schema
-        adducts_df = pl.DataFrame({
-            'name': [],
-            'charge': [],
-            'mass_shift': [],
-            'probability': [],
-            'complexity': []
-        })
-    
+        adducts_df = pl.DataFrame(
+            {
+                "name": [],
+                "charge": [],
+                "mass_shift": [],
+                "probability": [],
+                "complexity": [],
+            },
+        )
+
     return adducts_df
 
+
 def _calculate_formula_mass_shift(self, formula: str) -> float:
     """Calculate mass shift from formula string like "+H", "-H2O", "+Na-H", etc."""
     # Standard atomic masses
     atomic_masses = {
-        'H': 1.007825,
-        'C': 12.0,
-        'N': 14.003074,
-        'O': 15.994915,
-        'Na': 22.989769,
-        'K': 38.963707,
-        'Li': 7.016003,
-        'Ca': 39.962591,
-        'Mg': 23.985042,
-        'Fe': 55.934938,
-        'Cl': 34.968853,
-        'Br': 78.918336,
-        'I': 126.904473,
-        'P': 30.973762,
-        'S': 31.972071
+        "H": 1.007825,
+        "C": 12.0,
+        "N": 14.003074,
+        "O": 15.994915,
+        "Na": 22.989769,
+        "K": 38.963707,
+        "Li": 7.016003,
+        "Ca": 39.962591,
+        "Mg": 23.985042,
+        "Fe": 55.934938,
+        "Cl": 34.968853,
+        "Br": 78.918336,
+        "I": 126.904473,
+        "P": 30.973762,
+        "S": 31.972071,
     }
-    
+
     total_mass = 0.0
-    
+
     # Parse formula by splitting on + and - while preserving the operators
     parts = []
     current_part = ""
     current_sign = 1
-    
+
     for char in formula:
-        if char == '+':
+        if char == "+":
             if current_part:
                 parts.append((current_sign, current_part))
             current_part = ""
             current_sign = 1
-        elif char == '-':
+        elif char == "-":
             if current_part:
                 parts.append((current_sign, current_part))
             current_part = ""
             current_sign = -1
         else:
             current_part += char
-    
+
     if current_part:
         parts.append((current_sign, current_part))
-    
+
     # Process each part
     for sign, part in parts:
         if not part:
             continue
-            
+
         # Parse element and count (e.g., "H2O" -> H:2, O:1)
         elements = self._parse_element_counts(part)
-        
+
         for element, count in elements.items():
             if element in atomic_masses:
                 total_mass += sign * atomic_masses[element] * count
-    
+
     return total_mass
 
+
 def _parse_element_counts(self, formula_part: str) -> dict[str, int]:
     """Parse element counts from a formula part like 'H2O' -> {'H': 2, 'O': 1}"""
     elements = {}
     i = 0
-    
+
     while i < len(formula_part):
         # Get element (uppercase letter, possibly followed by lowercase)
         element = formula_part[i]
         i += 1
-        
+
         while i < len(formula_part) and formula_part[i].islower():
             element += formula_part[i]
             i += 1
-        
+
         # Get count (digits following element)
         count_str = ""
         while i < len(formula_part) and formula_part[i].isdigit():
             count_str += formula_part[i]
             i += 1
-        
+
         count = int(count_str) if count_str else 1
         elements[element] = elements.get(element, 0) + count
-    
+
     return elements
 
+
 def _format_adduct_name(self, components: list[dict]) -> str:
     """Format adduct name from components like [M+H]1+ or [M+2H]2+"""
     if not components:
         return "[M]"
-    
+
     # Count occurrences of each formula
     from collections import Counter
-    formula_counts = Counter(comp['formula'] for comp in components)
-    total_charge = sum(comp['charge'] for comp in components)
-    
+
+    formula_counts = Counter(comp["formula"] for comp in components)
+    total_charge = sum(comp["charge"] for comp in components)
+
     # Build formula part with proper multipliers
     formula_parts = []
-    for formula, count in sorted(formula_counts.items()):  # Sort for consistent ordering
+    for formula, count in sorted(
+        formula_counts.items(),
+    ):  # Sort for consistent ordering
         if count == 1:
             formula_parts.append(formula)
         else:
             # For multiple occurrences, use count prefix (e.g., 2H, 3Na)
             # Handle special case where formula might already start with + or -
-            if formula.startswith(('+', '-')):
+            if formula.startswith(("+", "-")):
                 sign = formula[0]
                 base_formula = formula[1:]
                 formula_parts.append(f"{sign}{count}{base_formula}")
             else:
                 formula_parts.append(f"{count}{formula}")
-    
+
     # Combine formula parts
     formula = "".join(formula_parts)
-    
+
     # Format charge
     if total_charge == 0:
         charge_str = ""
     elif abs(total_charge) == 1:
         charge_str = "1+" if total_charge > 0 else "1-"
     else:
-        charge_str = f"{abs(total_charge)}+" if total_charge > 0 else f"{abs(total_charge)}-"
-    
-    return f"[M{formula}]{charge_str}"
+        charge_str = (
+            f"{abs(total_charge)}+" if total_charge > 0 else f"{abs(total_charge)}-"
+        )
+
+    return f"[M{formula}]{charge_str}"