Update run.py with chromatogram access methods and update tox.ini for Python 3.12/3.13

Author: rkjulian

pymzml/run.py

@@ -183,26 +183,29 @@ def __next__(self):
 
     def __getitem__(self, identifier):
         """
-        Access spectrum with native id 'identifier'.
+        Access spectrum or chromatogram with native id 'identifier'.
 
         Arguments:
             identifier (str or int): last number in the id tag of the spectrum
-                element
+                element or a chromatogram identifier like 'TIC'
 
         Returns:
             spectrum (Spectrum or Chromatogram): spectrum/chromatogram object
             with native id 'identifier'
         """
         try:
-            if int(identifier) > self.get_spectrum_count():
+            if isinstance(identifier, int) and identifier > self.get_spectrum_count():
                 raise Exception("Requested identifier is out of range")
         except:
             pass
-        spectrum = self.info["file_object"][identifier]
-        spectrum.obo_translator = self.OT
-        if isinstance(spectrum, spec.Spectrum):
-            spectrum.measured_precision = self.ms_precisions[spectrum.ms_level]
-        return spectrum
+        
+        element = self.info["file_object"][identifier]
+        element.obo_translator = self.OT
+        
+        if isinstance(element, spec.Spectrum):
+            element.measured_precision = self.ms_precisions[element.ms_level]
+        
+        return element
 
     def __enter__(self):
         return self
@@ -454,6 +457,74 @@ def get_chromatogram_count(self):
             chromatogram count (int): Number of chromatograms in file.
         """
         return self.info["chromatogram_count"]
+        
+    def get_spectrum(self, identifier):
+        """
+        Access spectrum with the given identifier.
+        
+        Arguments:
+            identifier (str or int): Either a string identifier or an index (0-based)
+                to access spectra in order.
+                
+        Returns:
+            spectrum (Spectrum): spectrum object with the given identifier
+            
+        Note:
+            This method provides the same functionality as using the indexing syntax
+            (e.g., run[0]), but with a more explicit method name.
+        """
+        return self[identifier]
+        
+    def get_chromatogram(self, identifier):
+        """
+        Access chromatogram with the given identifier.
+        
+        Arguments:
+            identifier (str or int): Either a string identifier like 'TIC' or
+                an index (0-based) to access chromatograms in order.
+                
+        Returns:
+            chromatogram (Chromatogram): chromatogram object with the given identifier
+            
+        Note:
+            This method is only useful when skip_chromatogram is set to False
+            if you want to access chromatograms by index. If skip_chromatogram is True,
+            you can still access chromatograms by string identifiers (e.g., 'TIC').
+        """
+        if isinstance(identifier, str):
+            return self[identifier]
+            
+        if isinstance(identifier, int):
+            if self.get_chromatogram_count() is None:
+                raise Exception("No chromatograms found in the file")
+                
+            if identifier >= self.get_chromatogram_count():
+                raise Exception(f"Chromatogram index {identifier} is out of range (0-{self.get_chromatogram_count()-1})")
+                
+            # Reset the file pointer and iterate to find the chromatogram
+            temp_skip_chromatogram = self.skip_chromatogram
+            self.skip_chromatogram = False
+            
+            self.info["file_object"].close()
+            self.info["file_object"] = self._open_file(
+                self.path_or_file, build_index_from_scratch=False
+            )
+            self.iter = self._init_iter()
+            
+            chrom_count = 0
+            try:
+                for element in self:
+                    if isinstance(element, spec.Chromatogram):
+                        if chrom_count == identifier:
+                            return element
+                        chrom_count += 1
+            finally:
+                # Restore original skip_chromatogram setting
+                self.skip_chromatogram = temp_skip_chromatogram
+                
+            raise Exception(f"Chromatogram with index {identifier} not found")
+        
+        raise ValueError("Identifier must be a string or an integer")
 
     def close(self):
         self.info["file_object"].close()

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py37,py38,py39,coverage,example_scripts,docu
+envlist = py37,py38,py39,py312,py313,coverage,example_scripts,docu
 
 [testenv]
 deps =
@@ -48,6 +48,7 @@ deps =
 commands =
   pip install -Ur{toxinidir}/requirements.txt
   python example_scripts/access_run_info.py
+  python example_scripts/access_spectra_and_chromatograms.py
   python example_scripts/compare_spectra.py
   python example_scripts/extract_ion_chromatogram.py
   python example_scripts/extreme_values.py