make helper more visible

Author: florian-huber

ms2query/spectral_processing/__init__.py

@@ -1,7 +1,8 @@
-from .merging_utils import cluster_block, get_merged_spectra
+from .merging_utils import cluster_block, get_merged_spectra, normalize_spectrum_sum
 
 
 __all__ = [
     "cluster_block",
     "get_merged_spectra",
+    "normalize_spectrum_sum",
 ]

ms2query/spectral_processing/merging_utils.py

@@ -13,13 +13,14 @@
 
 
 # --------------------- Helper functions ---------------------
-def _normalize_spectrum_sum(s):
-    """Return a *copy* of s with intensities normalized to sum=1 (if possible)."""
+def normalize_spectrum_sum(s):
+    """Return a spectrum with intensities normalized to sum=1 (if possible)."""
     mz = np.asarray(s.peaks.mz, dtype=float)
     intens = np.asarray(s.peaks.intensities, dtype=float)
     tot = intens.sum()
     if tot > 0:
         intens = intens / tot
+
     # Build a shallow copy with normalized peaks but same metadata
     md = dict(s.metadata) if hasattr(s, "metadata") else {}
     return Spectrum(mz=mz, intensities=intens, metadata=md)
@@ -39,10 +40,10 @@ def _merge_cluster_to_consensus(cluster_spectra, mz_tol=0.01, min_frac=0.25):
     n = len(cluster_spectra)
     if n == 1:
         # Shouldn’t happen here, but keep it safe.
-        return _normalize_spectrum_sum(cluster_spectra[0])
+        return normalize_spectrum_sum(cluster_spectra[0])
 
     # Normalize each spectrum (sum=1)
-    specs = [_normalize_spectrum_sum(s) for s in cluster_spectra]
+    specs = [normalize_spectrum_sum(s) for s in cluster_spectra]
 
     # Collect all peaks with a spectrum index
     all_mz = []
@@ -195,7 +196,7 @@ def get_merged_spectra(spectra, clusters, mz_tol=0.01, min_frac=0.25):
             spectra_new.append(merged)
         else:
             # singletons: normalize to sum=1 for consistency
-            spectra_new.append(_normalize_spectrum_sum(spectra[cluster[0]]))
+            spectra_new.append(normalize_spectrum_sum(spectra[cluster[0]]))
     return spectra_new
 
 

tests/test_merging_utils.py

@@ -6,7 +6,7 @@
 
 # Adjust if your module name is different:
 from ms2query.spectral_processing.merging_utils import (
-    _normalize_spectrum_sum,
+    normalize_spectrum_sum,
     _merge_cluster_to_consensus,
     get_merged_spectra,
 )
@@ -23,7 +23,7 @@ def spec(mz, intensities, **metadata):
 
 def test_normalize_spectrum_sum():
     s = spec([100, 150], [10, 5])
-    sn = _normalize_spectrum_sum(s)
+    sn = normalize_spectrum_sum(s)
     assert pytest.approx(sn.peaks.intensities.sum()) == 1.0
     # Same mz layout
     assert_allclose(sn.peaks.mz, [100, 150])