Ignore empty spectra

ms2pip/core.py

@@ -846,8 +846,8 @@ def _process_spectra(
             spectrum_id = match[1]
         except (TypeError, IndexError):
             raise exceptions.TitlePatternError(
-                "Spectrum title pattern could not be matched to spectrum IDs "
-                f"`{spectrum.identifier}`. "
+                f"Spectrum title pattern `{spectrum_id_pattern}` could not be matched to "
+                f"spectrum ID `{spectrum.identifier}`. "
                 " Are you sure that the regex contains a capturing group?"
             )
 

ms2pip/spectrum_input.py

@@ -34,14 +34,22 @@ def read_spectrum_file(spectrum_file: str) -> Generator[ObservedSpectrum, None,
         raise UnsupportedSpectrumFiletypeError(file_extension)
 
     for spectrum in get_ms2_spectra(str(spectrum_file)):
-        yield ObservedSpectrum(
+        obs_spectrum = ObservedSpectrum(
             mz=np.array(spectrum.mz, dtype=np.float32),
             intensity=np.array(spectrum.intensity, dtype=np.float32),
             identifier=str(spectrum.identifier),
             precursor_mz=float(spectrum.precursor.mz),
             precursor_charge=float(spectrum.precursor.charge),
             retention_time=float(spectrum.precursor.rt),
         )
+        # Workaround for mobiusklein/mzdata#3
+        if (
+            obs_spectrum.identifier == ""
+            or obs_spectrum.mz.shape[0] == 0
+            or obs_spectrum.intensity.shape[0] == 0
+        ):
+            continue
+        yield obs_spectrum
 
 
 def _is_minitdf(spectrum_file: str) -> bool: