Lint

Author: domdfcoding

pyms_lc_esi/adducts.py

@@ -33,7 +33,7 @@
 import attr
 from chemistry_tools.elements import ELEMENTS
 from chemistry_tools.formulae import Formula
-from pyms.Spectrum import MassSpectrum  # type: ignore[import]
+from pyms.Spectrum import MassSpectrum
 
 # this package
 from pyms_lc_esi.spectra import iso_dist_2_mass_spec
@@ -59,7 +59,7 @@ def _formula_converter(formula: Union[Dict[str, int], Formula, str]) -> Formula:
 		raise TypeError(f"Unsupported type for formula: {type(formula)}")
 
 
-def _operation_validator(instance, attribute, value: Literal["add", "sub"]) -> Literal["add", "sub"]:
+def _operation_validator(instance: "Adduct", attribute: attr.Attribute, value: Literal["add", "sub"]) -> Literal["add", "sub"]:
 	if not isinstance(value, str):
 		raise TypeError(f"operation must be a string, not {type(value)}")
 
@@ -111,7 +111,7 @@ def __call__(self, formula: Formula) -> Formula:
 	def __format__(self, format_spec: str) -> str:
 		return self.name % format_spec
 
-	def __mod__(self, other) -> str:
+	def __mod__(self, other: str) -> str:
 		return self.name % other
 
 

pyms_lc_esi/peak_finder.py

@@ -33,11 +33,11 @@
 # 3rd party
 from chemistry_tools.formulae import Formula
 from domdf_python_tools.words import word_join
-from pyms.BillerBiemann import get_maxima_indices, num_ions_threshold  # type: ignore[import]
-from pyms.eic import ExtractedIntensityMatrix, build_extracted_intensity_matrix  # type: ignore[import]
-from pyms.IntensityMatrix import IntensityMatrix  # type: ignore[import]
-from pyms.Noise.Analysis import window_analyzer  # type: ignore[import]
-from pyms.Peak import Peak  # type: ignore[import]
+from pyms.BillerBiemann import get_maxima_indices, num_ions_threshold
+from pyms.eic import ExtractedIntensityMatrix, build_extracted_intensity_matrix
+from pyms.IntensityMatrix import IntensityMatrix
+from pyms.Noise.Analysis import window_analyzer
+from pyms.Peak import Peak
 
 # this package
 from pyms_lc_esi.adducts import Adduct, get_adduct_spectra
@@ -185,7 +185,7 @@ def peak_finder(e_im: ExtractedIntensityMatrix, points: int = 3) -> Iterator[Pea
 		peak.area, left_bound, right_bound = sum_area(apex_index, e_im)
 
 		# Assign bounds to peak as offsets.
-		peak.bounds = [apex_index - left_bound, apex_index, right_bound - apex_index]
+		peak.bounds = (apex_index - left_bound, apex_index, right_bound - apex_index)
 
 		if (right_bound - left_bound) > 3 and peak.area > 1000:
 			# TODO: make 1000 dependent on data

pyms_lc_esi/spectra.py

@@ -39,7 +39,7 @@
 # from pyms import Peak
 # from pyms.IntensityMatrix import BaseIntensityMatrix
 # from pyms.Spectrum import CompositeMassSpectrum, MassSpectrum, normalize_mass_spec
-from pyms.Spectrum import MassSpectrum  # type: ignore[import]
+from pyms.Spectrum import MassSpectrum
 
 __all__ = ["iso_dist_2_mass_spec"]