masster 0.3.15__py3-none-any.whl → 0.3.16__py3-none-any.whl

masster/sample/sample.py

@@ -49,6 +49,7 @@ from masster.sample.defaults.get_spectrum_def import get_spectrum_defaults
 
 # Sample-specific imports
 from masster.sample.h5 import _load_sample5
+from masster.sample.h5 import _load_sample5_study
 from masster.sample.h5 import _save_sample5
 from masster.sample.helpers import _delete_ms2
 from masster.sample.helpers import _estimate_memory_usage
@@ -72,6 +73,7 @@ from masster.sample.load import _load_wiff
 from masster.sample.load import chrom_extract
 from masster.sample.load import index_file
 from masster.sample.load import load
+from masster.sample.load import load_study
 from masster.sample.load import sanitize
 from masster.sample.plot import plot_2d
 from masster.sample.plot import plot_2d_oracle
@@ -203,6 +205,7 @@ class Sample:
 
     # Attach module functions as class methods
     load = load
+    load_study = load_study
     save = save
     find_features = find_features
     find_adducts = find_adducts
@@ -243,6 +246,7 @@ class Sample:
 
     # Additional method assignments for all imported functions
     _load_sample5 = _load_sample5
+    _load_sample5_study = _load_sample5_study
     _save_sample5 = _save_sample5
     _delete_ms2 = _delete_ms2
     _estimate_memory_usage = _estimate_memory_usage

masster/spectrum.py

@@ -229,6 +229,9 @@ class Spectrum:
             elif isinstance(value, (list, dict)):
                 # Create copies of mutable objects
                 result[key] = copy.deepcopy(value)
+            elif isinstance(value, np.number):
+                # Handle numpy scalar types (float32, int32, etc.)
+                result[key] = value.item()
             else:
                 # Immutable objects can be copied directly
                 result[key] = value

masster/study/defaults/fill_def.py

@@ -23,7 +23,7 @@ class fill_defaults:
     uids: Optional[list] = None
     mz_tol: float = 0.010
     rt_tol: float = 10.0
-    min_samples_rel: float = 0.05
+    min_samples_rel: float = 0.00
     min_samples_abs: int = 5
 
     _param_metadata: dict[str, dict[str, Any]] = field(
@@ -37,7 +37,7 @@ class fill_defaults:
                 "dtype": float,
                 "description": "m/z tolerance for chromatogram extraction (Da)",
                 "default": 0.010,
-                "min_value": 0.001,
+                "min_value": 0.0002,
                 "max_value": 0.1,
             },
             "rt_tol": {
@@ -51,7 +51,7 @@ class fill_defaults:
                 "dtype": float,
                 "description": "Minimum relative samples threshold (fraction)",
                 "default": 0.05,
-                "min_value": 0.01,
+                "min_value": 0.0,
                 "max_value": 1.0,
             },
             "min_samples_abs": {

masster/study/export.py

@@ -180,6 +180,9 @@ def _get_mgf_df(self, **kwargs):
             for e in energies:
                 cons_ms2_e = cons_ms2[cons_ms2["energy"] == e]
                 if selection == "best":
+                    # Check if the filtered DataFrame is empty
+                    if len(cons_ms2_e) == 0:
+                        continue
                     idx = cons_ms2_e["prec_inty"].idxmax()
                     cons_ms2_e_row = cons_ms2_e.loc[idx]
                     spect = cons_ms2_e_row["spec"]