Avoid chained assignment when filling spectrum columns

alpharaw/ms_data_base.py

@@ -410,7 +410,7 @@ def add_column_in_spec_df_by_spec_idxes(
         na_value=np.nan,
     ):
         self.spectrum_df.loc[spec_idxes, column_name] = values
-        self.spectrum_df[column_name].fillna(na_value, inplace=True)
+        self.spectrum_df[column_name] = self.spectrum_df[column_name].fillna(na_value)
         self.spectrum_df[column_name] = self.spectrum_df[column_name].astype(dtype)
 
     def add_column_in_df_by_scan_num(

tests/unit/test_ms_data_base.py

@@ -0,0 +1,23 @@
+import warnings
+
+import numpy as np
+
+from alpharaw.ms_data_base import MSData_Base
+
+
+def test_add_column_in_spec_df_avoids_chained_assignment_warning():
+    ms_data = MSData_Base()
+    ms_data.create_spectrum_df(3)
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", FutureWarning)
+        ms_data.add_column_in_spec_df_by_spec_idxes(
+            "ms_level",
+            np.array([2, 3]),
+            np.array([0, 2]),
+            dtype=np.int8,
+            na_value=1,
+        )
+
+    np.testing.assert_array_equal(ms_data.spectrum_df["ms_level"], [2, 1, 3])
+    assert ms_data.spectrum_df["ms_level"].dtype == np.int8