masster 0.4.0__py3-none-any.whl → 0.4.1__py3-none-any.whl

masster/sample/sciex.py

@@ -262,9 +262,7 @@ class SciexWiff2FileReader:
             self._alpharaw_reader.import_raw(self.filename)
 
             # Extract basic information (SciexWiffData doesn't have sample_names property)
-            self.sample_names = [
-                "Sample_0",
-            ]  # Default since WIFF2 format needs investigation
+            self.sample_names = ["Sample_0"]  # Default since WIFF2 format needs investigation
             self.sample_count = 1
             self.initialization_method = "alpharaw_SciexWiffData"
 
@@ -356,9 +354,7 @@ class SciexWiff2FileReader:
             # Get metadata from alpharaw reader
             try:
                 if hasattr(self._alpharaw_reader, "get_spectrum_count"):
-                    metadata["total_spectra"] = (
-                        self._alpharaw_reader.get_spectrum_count()
-                    )
+                    metadata["total_spectra"] = self._alpharaw_reader.get_spectrum_count()
 
                 # Add alpharaw-specific metadata
                 for attr in ["creation_time", "instrument_model", "ms_levels"]:
@@ -388,9 +384,7 @@ class SciexWiff2FileReader:
                     if hasattr(sample, "Details"):
                         details = sample.Details
                         if hasattr(details, "AcquisitionDateTime"):
-                            sample_info["acquisition_time"] = str(
-                                details.AcquisitionDateTime.ToString("O"),
-                            )
+                            sample_info["acquisition_time"] = str(details.AcquisitionDateTime.ToString("O"))
 
                     if hasattr(sample, "MassSpectrometerSample"):
                         ms_sample = sample.MassSpectrometerSample
@@ -440,29 +434,15 @@ class SciexWiff2FileReader:
 
             # Convert to the expected format
             spectral_data = {
-                "peak_indices": spectrum_df[
-                    ["peak_start_idx", "peak_stop_idx"]
-                ].values.flatten(),
+                "peak_indices": spectrum_df[["peak_start_idx", "peak_stop_idx"]].values.flatten(),
                 "peak_mz": peak_df["mz"].values,
                 "peak_intensity": peak_df["intensity"].values,
                 "rt": spectrum_df["rt"].values,
                 "ms_level": spectrum_df["ms_level"].values,
-                "precursor_mz": spectrum_df.get(
-                    "precursor_mz",
-                    np.full(len(spectrum_df), -1.0),
-                ).values,
-                "precursor_charge": spectrum_df.get(
-                    "precursor_charge",
-                    np.full(len(spectrum_df), 0),
-                ).values,
-                "isolation_lower_mz": spectrum_df.get(
-                    "isolation_lower_mz",
-                    np.full(len(spectrum_df), -1.0),
-                ).values,
-                "isolation_upper_mz": spectrum_df.get(
-                    "isolation_upper_mz",
-                    np.full(len(spectrum_df), -1.0),
-                ).values,
+                "precursor_mz": spectrum_df.get("precursor_mz", np.full(len(spectrum_df), -1.0)).values,
+                "precursor_charge": spectrum_df.get("precursor_charge", np.full(len(spectrum_df), 0)).values,
+                "isolation_lower_mz": spectrum_df.get("isolation_lower_mz", np.full(len(spectrum_df), -1.0)).values,
+                "isolation_upper_mz": spectrum_df.get("isolation_upper_mz", np.full(len(spectrum_df), -1.0)).values,
                 "nce": spectrum_df.get("nce", np.full(len(spectrum_df), 0.0)).values,
                 "metadata": {
                     "format": "WIFF2",
@@ -475,10 +455,7 @@ class SciexWiff2FileReader:
                     "total_peaks": len(peak_df),
                     "ms1_count": np.sum(spectrum_df["ms_level"] == 1),
                     "ms2_count": np.sum(spectrum_df["ms_level"] > 1),
-                    "rt_range": [
-                        float(spectrum_df["rt"].min()),
-                        float(spectrum_df["rt"].max()),
-                    ]
+                    "rt_range": [float(spectrum_df["rt"].min()), float(spectrum_df["rt"].max())]
                     if len(spectrum_df) > 0
                     else [0, 0],
                     "reader_method": "alpharaw",
@@ -501,9 +478,7 @@ class SciexWiff2FileReader:
         }
 
         if sample_id < 0 or sample_id >= self.sample_count:
-            raise ValueError(
-                f"Sample ID {sample_id} out of range (0-{self.sample_count - 1})",
-            )
+            raise ValueError(f"Sample ID {sample_id} out of range (0-{self.sample_count - 1})")
 
         # Use the same loading approach as SciexWiffFileReader but with enhancements
         sample = self._wiff_file.GetSample(sample_id)
@@ -521,9 +496,7 @@ class SciexWiff2FileReader:
         isolation_lower_list: list[float] = []
         isolation_upper_list: list[float] = []
 
-        exp_list = [
-            ms_sample.GetMSExperiment(i) for i in range(ms_sample.ExperimentCount)
-        ]
+        exp_list = [ms_sample.GetMSExperiment(i) for i in range(ms_sample.ExperimentCount)]
 
         for j in range(exp_list[0].Details.NumberOfScans):
             for i in range(ms_sample.ExperimentCount):
@@ -542,9 +515,7 @@ class SciexWiff2FileReader:
                     continue
 
                 mz_array = dot_net_array_to_np_array(mass_spectrum.GetActualXValues())
-                int_array = dot_net_array_to_np_array(
-                    mass_spectrum.GetActualYValues(),
-                ).astype(np.float32)
+                int_array = dot_net_array_to_np_array(mass_spectrum.GetActualYValues()).astype(np.float32)
 
                 if enhanced_params["centroid"]:
                     mz_array, int_array = naive_centroid(
@@ -554,9 +525,7 @@ class SciexWiff2FileReader:
                     )
 
                 if len(mz_array) > enhanced_params["keep_k_peaks"]:
-                    top_indices = np.argsort(int_array)[
-                        -enhanced_params["keep_k_peaks"] :
-                    ]
+                    top_indices = np.argsort(int_array)[-enhanced_params["keep_k_peaks"] :]
                     top_indices = np.sort(top_indices)
                     mz_array = mz_array[top_indices]
                     int_array = int_array[top_indices]
@@ -578,9 +547,7 @@ class SciexWiff2FileReader:
                             from WiffOps4Python import WiffOps as DotNetWiffOps
 
                             center_mz = DotNetWiffOps.get_center_mz(details)
-                            isolation_window = DotNetWiffOps.get_isolation_window(
-                                details,
-                            )
+                            isolation_window = DotNetWiffOps.get_isolation_window(details)
                         except:
                             center_mz = mass_spectrum_info.ParentMZ
                             isolation_window = 3.0
@@ -610,9 +577,7 @@ class SciexWiff2FileReader:
         return {
             "peak_indices": peak_indices,
             "peak_mz": np.concatenate(peak_mz_list) if peak_mz_list else np.array([]),
-            "peak_intensity": np.concatenate(peak_intensity_list)
-            if peak_intensity_list
-            else np.array([]),
+            "peak_intensity": np.concatenate(peak_intensity_list) if peak_intensity_list else np.array([]),
             "rt": np.array(rt_list, dtype=np.float64),
             "ms_level": np.array(ms_level_list, dtype=np.int8),
             "precursor_mz": np.array(precursor_mz_list, dtype=np.float64),
@@ -629,9 +594,7 @@ class SciexWiff2FileReader:
                 "total_peaks": sum(_peak_indices),
                 "ms1_count": np.sum(np.array(ms_level_list) == 1),
                 "ms2_count": np.sum(np.array(ms_level_list) > 1),
-                "rt_range": [float(np.min(rt_list)), float(np.max(rt_list))]
-                if rt_list
-                else [0, 0],
+                "rt_range": [float(np.min(rt_list)), float(np.max(rt_list))] if rt_list else [0, 0],
                 "creation_time": str(sample.Details.AcquisitionDateTime.ToString("O"))
                 if hasattr(sample, "Details")
                 else "",
@@ -733,10 +696,7 @@ class SciexWiffFileReader:
         isolation_lower_mz_list: list[float] = []
         isolation_upper_mz_list: list[float] = []
 
-        exp_list = [
-            self.msSample.GetMSExperiment(i)
-            for i in range(self.msSample.ExperimentCount)
-        ]
+        exp_list = [self.msSample.GetMSExperiment(i) for i in range(self.msSample.ExperimentCount)]
 
         for j in range(exp_list[0].Details.NumberOfScans):
             for i in range(self.msSample.ExperimentCount):
@@ -746,12 +706,7 @@ class SciexWiffFileReader:
                 details = exp.Details
                 ms_level = mass_spectrum_info.MSLevel
 
-                if (
-                    ms_level > 1
-                    and not details.IsSwath
-                    and mass_spectrum.NumDataPoints <= 0
-                    and ignore_empty_scans
-                ):
+                if ms_level > 1 and not details.IsSwath and mass_spectrum.NumDataPoints <= 0 and ignore_empty_scans:
                     continue
 
                 mz_array = dot_net_array_to_np_array(mass_spectrum.GetActualXValues())
@@ -915,9 +870,7 @@ class SciexWiffData:
             ignore_empty_scans=self.ignore_empty_scans,
             keep_k_peaks=self.keep_k_peaks_per_spec,
         )
-        self.creation_time = (
-            wiff_reader.wiffSample.Details.AcquisitionDateTime.ToString("O")
-        )
+        self.creation_time = wiff_reader.wiffSample.Details.AcquisitionDateTime.ToString("O")
         wiff_reader.close()
         return data_dict
 

masster/spectrum.py

@@ -138,7 +138,7 @@ class Spectrum:
 
     Example Usage:
         >>> import numpy as np
-        >>> from master import spec
+        >>> from masster import spec
         >>> mz = np.array([100.0, 150.0, 200.0, 250.0])
         >>> intensity = np.array([1000, 5000, 3000, 800])
         >>> spectrum = spec(mz=mz, inty=intensity, ms_level=1)
@@ -278,9 +278,7 @@ class Spectrum:
 
     def pandalize(self):
         data = {
-            key: val
-            for key, val in self.__dict__.items()
-            if isinstance(val, np.ndarray) and val.size == self.mz.size
+            key: val for key, val in self.__dict__.items() if isinstance(val, np.ndarray) and val.size == self.mz.size
         }
         return pd.DataFrame(data)
 
@@ -303,20 +301,14 @@ class Spectrum:
             self.mz = self.mz[mask]
             self.inty = self.inty[mask]
             for key in self.__dict__:
-                if (
-                    isinstance(self.__dict__[key], np.ndarray)
-                    and self.__dict__[key].size == mask.size
-                ):
+                if isinstance(self.__dict__[key], np.ndarray) and self.__dict__[key].size == mask.size:
                     self.__dict__[key] = self.__dict__[key][mask]
         if mz_max is not None:
             mask = self.mz <= mz_max
             self.mz = self.mz[mask]
             self.inty = self.inty[mask]
             for key in self.__dict__:
-                if (
-                    isinstance(self.__dict__[key], np.ndarray)
-                    and self.__dict__[key].size == mask.size
-                ):
+                if isinstance(self.__dict__[key], np.ndarray) and self.__dict__[key].size == mask.size:
                     self.__dict__[key] = self.__dict__[key][mask]
         return self
 
@@ -434,10 +426,7 @@ class Spectrum:
         mask = self_c.inty > threshold
         length = self_c.mz.size
         for key in self_c.__dict__:
-            if (
-                isinstance(self_c.__dict__[key], np.ndarray)
-                and self_c.__dict__[key].size == length
-            ):
+            if isinstance(self_c.__dict__[key], np.ndarray) and self_c.__dict__[key].size == length:
                 self_c.__dict__[key] = self_c.__dict__[key][mask]
         self_c.history_add("t[BL]")
         self_c.bl = threshold
@@ -478,10 +467,7 @@ class Spectrum:
             spec_obj.history_add("f[eic_corr_max]")
         mask_length = len(mask)
         for key in spec_obj.__dict__:
-            if (
-                isinstance(spec_obj.__dict__[key], np.ndarray)
-                and spec_obj.__dict__[key].size == mask_length
-            ):
+            if isinstance(spec_obj.__dict__[key], np.ndarray) and spec_obj.__dict__[key].size == mask_length:
                 spec_obj.__dict__[key] = spec_obj.__dict__[key][mask]
         return spec_obj
 
@@ -564,16 +550,12 @@ class Spectrum:
                 s.history_add("s[SG]")
             case "cumsum":
                 cumsum_vec = np.cumsum(np.insert(s.inty, 0, 0))
-                ma_vec = (
-                    cumsum_vec[window_length:] - cumsum_vec[:-window_length]
-                ) / window_length
-                s.inty = np.concatenate(
-                    (
-                        s.inty[: window_length // 2],
-                        ma_vec,
-                        s.inty[-window_length // 2 :],
-                    ),
-                )
+                ma_vec = (cumsum_vec[window_length:] - cumsum_vec[:-window_length]) / window_length
+                s.inty = np.concatenate((
+                    s.inty[: window_length // 2],
+                    ma_vec,
+                    s.inty[-window_length // 2 :],
+                ))
                 s.history_add("s[CSM]")
                 s.history_add("s[CSM]")
         return s
@@ -707,9 +689,7 @@ class Spectrum:
                 i += 1
         mask = np.where(is_isotopolog_of == 0)[0]
         for key in self_c.__dict__:
-            if isinstance(self_c.__dict__[key], np.ndarray) and self_c.__dict__[
-                key
-            ].size == len(is_isotopolog_of):
+            if isinstance(self_c.__dict__[key], np.ndarray) and self_c.__dict__[key].size == len(is_isotopolog_of):
                 self_c.__dict__[key] = self_c.__dict__[key][mask]
         if self_c.label is not None:
             self_c.label = self_c.label + " deiso."
@@ -749,9 +729,7 @@ class Spectrum:
                 cvalues = (cvalues - cmap_min) / (cmap_max - cmap_min) * 255
                 cm = process_cmap(cmap, ncolors=255, provider=cmap_provider)
                 colors = [
-                    rgb2hex(cm[int(i * (len(cm) - 1) / 255)])
-                    if not np.isnan(i)
-                    else rgb2hex((0, 0, 0))
+                    rgb2hex(cm[int(i * (len(cm) - 1) / 255)]) if not np.isnan(i) else rgb2hex((0, 0, 0))
                     for i in cvalues
                 ]
         p = figure(
@@ -801,11 +779,7 @@ class Spectrum:
             p.line(mz, inty, line_color="black", legend_label=label)
         else:
             data = self.to_dict()
-            data = {
-                key: val
-                for key, val in data.items()
-                if isinstance(val, np.ndarray) and val.size == mz.size
-            }
+            data = {key: val for key, val in data.items() if isinstance(val, np.ndarray) and val.size == mz.size}
             if ylog:
                 data["zeros"] = np.ones_like(mz)
             else:
@@ -844,9 +818,7 @@ class Spectrum:
             tooltips = [(k, "@" + k) for k in source.data if k != "zeros"]
             hover_tool = HoverTool(renderers=[sc], tooltips=tooltips)
             p.add_tools(hover_tool)
-            box_zoom_tools = [
-                tool for tool in p.toolbar.tools if isinstance(tool, BoxZoomTool)
-            ]
+            box_zoom_tools = [tool for tool in p.toolbar.tools if isinstance(tool, BoxZoomTool)]
             if box_zoom_tools:
                 p.toolbar.active_drag = box_zoom_tools[0]
             if colorby is not None:
@@ -1001,9 +973,7 @@ def combine_peaks(
         all_inty = np.concatenate([pm.inty for pm in spectra])
 
         # Track which spectrum each peak came from
-        spectrum_indices = np.concatenate(
-            [np.full(len(pm.mz), i) for i, pm in enumerate(spectra)],
-        )
+        spectrum_indices = np.concatenate([np.full(len(pm.mz), i) for i, pm in enumerate(spectra)])
 
     if all_mz.size < 2:
         return Spectrum(
@@ -1137,9 +1107,7 @@ def plot_spectra(
     num_plots = len(spectra)
     cm = process_cmap(cmap, ncolors=num_plots, provider=cmap_provider)
     colors = [
-        rgb2hex(cm[int(i * (len(cm) - 1) / (num_plots - 1))])
-        if num_plots > 1
-        else rgb2hex(cm[0])
+        rgb2hex(cm[int(i * (len(cm) - 1) / (num_plots - 1))]) if num_plots > 1 else rgb2hex(cm[0])
         for i in range(num_plots)
     ]
 
@@ -1237,11 +1205,7 @@ def plot_spectra(
                 # For centroided spectra, build a data source that includes all available array attributes
                 data = spec.to_dict()
                 # remove all keys whose value does not have the size of mz
-                data = {
-                    key: val
-                    for key, val in data.items()
-                    if isinstance(val, np.ndarray) and val.size == mz.size
-                }
+                data = {key: val for key, val in data.items() if isinstance(val, np.ndarray) and val.size == mz.size}
                 data["zeros"] = np.zeros_like(mz)
                 if colorby is not None:
                     data[colorby] = mcolors
@@ -1280,9 +1244,7 @@ def plot_spectra(
                 tooltips = [(k, "@" + k) for k in source.data if k != "zeros"]
                 hover_tool = HoverTool(renderers=[sc], tooltips=tooltips)  # seg
                 p.add_tools(hover_tool)
-                box_zoom_tools = [
-                    tool for tool in p.toolbar.tools if isinstance(tool, BoxZoomTool)
-                ]
+                box_zoom_tools = [tool for tool in p.toolbar.tools if isinstance(tool, BoxZoomTool)]
                 if box_zoom_tools:
                     p.toolbar.active_drag = box_zoom_tools[0]
         except Exception as e:

masster/study/__init__.py

@@ -1,5 +1,5 @@
 """
-Study module for master.
+Study module for masster.
 
 This module provides the Sample class for handling mass spectrometry data.
 """

masster/study/defaults/align_def.py

@@ -298,11 +298,7 @@ class align_defaults:
                 "dtype": str,
                 "description": "Method to use for extrapolation outside the data range in LOWESS",
                 "default": "four-point-linear",
-                "allowed_values": [
-                    "two-point-linear",
-                    "four-point-linear",
-                    "global-linear",
-                ],
+                "allowed_values": ["two-point-linear", "four-point-linear", "global-linear"],
             },
         },
         repr=False,

masster/study/defaults/fill_chrom_def.py

@@ -168,11 +168,7 @@ class fill_chrom_defaults:
             expected_dtype = self._param_metadata[param_name]["dtype"]
 
             # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
+            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
                 if "int" in expected_dtype and not isinstance(value, int):
                     try:
                         value = int(value)

masster/study/defaults/fill_def.py

@@ -168,11 +168,7 @@ class fill_defaults:
             expected_dtype = self._param_metadata[param_name]["dtype"]
 
             # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
+            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
                 if "int" in expected_dtype and not isinstance(value, int):
                     try:
                         value = int(value)

masster/study/defaults/integrate_chrom_def.py

@@ -135,11 +135,7 @@ class integrate_chrom_defaults:
             expected_dtype = self._param_metadata[param_name]["dtype"]
 
             # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
+            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
                 if "float" in expected_dtype and not isinstance(value, float):
                     try:
                         value = float(value)

masster/study/defaults/integrate_def.py

@@ -135,11 +135,7 @@ class integrate_defaults:
             expected_dtype = self._param_metadata[param_name]["dtype"]
 
             # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
+            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
                 if "float" in expected_dtype and not isinstance(value, float):
                     try:
                         value = float(value)

masster/study/defaults/study_def.py

@@ -33,7 +33,7 @@ class study_defaults:
 
     eic_mz_tol: float = 0.01
     eic_rt_tol: float = 10.0
-
+    
     polarity: str = "positive"
     adducts: list[str] | None = None
     adduct_min_probability: float = 0.04
@@ -54,14 +54,7 @@ class study_defaults:
                 "dtype": str,
                 "description": "Logging level to be set for the logger",
                 "default": "INFO",
-                "allowed_values": [
-                    "TRACE",
-                    "DEBUG",
-                    "INFO",
-                    "WARNING",
-                    "ERROR",
-                    "CRITICAL",
-                ],
+                "allowed_values": ["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
             },
             "log_label": {
                 "dtype": "Optional[str]",
@@ -99,19 +92,14 @@ class study_defaults:
                 "default": ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"],
                 "examples": {
                     "positive": ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"],
-                    "negative": [
-                        "H-1:-:0.95",
-                        "Cl:-:0.05",
-                        "CH2O2:0:0.2",
-                        "H-2-O:0:0.2",
-                    ],
+                    "negative": ["H-1:-:0.95", "Cl:-:0.05", "CH2O2:0:0.2", "H-2-O:0:0.2"]
                 },
                 "validation_rules": [
                     "Format: element:charge:probability",
                     "Charge must be +, -, or 0 (neutral)",
                     "Probability must be between 0.0 and 1.0",
-                    "Sum of all charged adduct probabilities must equal 1.0",
-                ],
+                    "Sum of all charged adduct probabilities must equal 1.0"
+                ]
             },
             "adduct_min_probability": {
                 "dtype": float,
@@ -128,71 +116,54 @@ class study_defaults:
         """Set polarity-specific defaults for adducts if not explicitly provided."""
         # If adducts is None, set based on polarity
         if self.adducts is None:
-            if self.polarity.lower() in ["positive", "pos"]:
-                self.adducts = [
-                    "+H:1:0.65",
-                    "+Na:1:0.15",
-                    "+NH4:1:0.15",
-                    "+K:1:0.05",
-                    "-H2O:0:0.15",
-                ]
-            elif self.polarity.lower() in ["negative", "neg"]:
-                self.adducts = [
-                    "-H:-1:0.9",
-                    "+Cl:-1:0.1",
-                    "+CH2O2:0:0.15",
-                    "-H2O:0:0.15",
-                ]
+            if self.polarity.lower() in ['positive', 'pos']:
+                self.adducts = ["+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.15"]
+            elif self.polarity.lower() in ['negative', 'neg']:
+                self.adducts = ["-H:-1:0.9", "+Cl:-1:0.1", "+CH2O2:0:0.15", "-H2O:0:0.15"]
             else:
                 # Default to positive if polarity is not recognized
-                self.adducts = [
-                    "+H:1:0.65",
-                    "+Na:1:0.15",
-                    "+NH4:1:0.15",
-                    "+K:1:0.05",
-                    "-H2O:0:0.15",
-                ]
+                self.adducts = ["+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.15"]
 
     def _validate_adducts(self, adduct_list: list[str]) -> bool:
         """
         Validate adducts according to OpenMS convention.
-
+        
         Format: element:charge:probability
         - Elements can be molecular formulas (e.g., H, Na, NH4, H-1, CH2O2)
         - Charge must be +, -, or 0 (for neutral)
         - Probability must be a float between 0 and 1
         - Total probability of all charged adducts should sum to 1.0
-
+        
         Args:
             adduct_list: List of adduct strings in OpenMS format
-
+            
         Returns:
             True if all adducts are valid, False otherwise
         """
         if not adduct_list:  # Empty list is valid
             return True
-
+            
         charged_total_prob = 0.0
         neutral_total_prob = 0.0
-
+        
         for adduct in adduct_list:
             if not isinstance(adduct, str):
                 return False
-
+                
             parts = adduct.split(":")
             if len(parts) != 3:
                 return False
-
+                
             element, charge, prob_str = parts
-
+            
             # Validate element (non-empty string)
             if not element:
                 return False
-
+                
             # Validate charge
             if charge not in ["+", "-", "0"]:
                 return False
-
+                
             # Validate probability
             try:
                 probability = float(prob_str)
@@ -200,20 +171,20 @@ class study_defaults:
                     return False
             except (ValueError, TypeError):
                 return False
-
+                
             # Sum probabilities by charge type
             if charge in ["+", "-"]:
                 charged_total_prob += probability
             else:  # charge == "0" (neutral)
                 neutral_total_prob += probability
-
+        
         # Validate probability constraints
         # Charged adducts should sum to 1.0 (within tolerance)
         if charged_total_prob > 0 and abs(charged_total_prob - 1.0) > 1e-6:
             return False
-
+            
         # Neutral adducts can have any total probability (they're optional)
-
+        
         return True
 
     def get_info(self, param_name: str) -> dict[str, Any]:
@@ -345,11 +316,7 @@ class study_defaults:
             expected_dtype = self._param_metadata[param_name]["dtype"]
 
             # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
+            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
                 if "int" in expected_dtype and not isinstance(value, int):
                     try:
                         value = int(value)