feature: change sign of the charge_range based on polarity peak list attribute in deconvolute_peaks (#34)

* updated the sign of the charge_range based on polairty of the scan in deconvolute_peaks function

---------

Co-authored-by: Joshua Klein <[email protected]>

Author: btemoshir

src/ms_deisotope/deconvolution/api.py

@@ -64,7 +64,7 @@ def deconvolute_peaks(peaklist: PeakListTypes,
         Parameters to use to initialize the deconvoluter instance produced by
         ``deconvoluter_type``
     charge_range : tuple of integers, optional
-        The range of charge states to consider. The range is inclusive.
+        The range of charge states to consider. The range is inclusive. Sensitive to sign of the charge/polarity.
     error_tolerance : float, optional
         PPM error tolerance to use to match experimental to theoretical peaks
     priority_list : list, optional
@@ -136,11 +136,17 @@ def deconvolute_peaks(peaklist: PeakListTypes,
     decon_config.setdefault("scale_method", SCALE_METHOD)
     decon_config.setdefault("use_quick_charge", use_quick_charge)
 
+    # Update the charge range with the proper sign, considering the polarity when
+    # the `polarity` attribute is defined on `peaklist`.
+    if hasattr(peaklist, 'polarity'):
+        polarity = int(peaklist.polarity)
+        if polarity < 0 and max(charge_range) > 0:
+            charge_range = tuple(c * polarity for c in charge_range)
+
     peaklist = prepare_peaklist(peaklist)
 
     decon = deconvoluter_type(peaklist=peaklist, **decon_config)
 
-
     if verbose_priorities or verbose:
         decon.verbose = True