fix: typing for python 3.9

fix typing references for python 3.9
Roestlab · Oct 9, 2024 · 844a4d1 · 844a4d1
1 parent 9756ae9
commit 844a4d1
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/massdash/loaders/GenericChromatogramLoader.py b/massdash/loaders/GenericChromatogramLoader.py
@@ -27,7 +27,7 @@ def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
     @abstractmethod
-    def loadTransitionGroups(self, pep_id: str, charge: int, runNames: None | str | List[str] ) -> Dict[str, TransitionGroup]:
+    def loadTransitionGroups(self, pep_id: str, charge: int, runNames: Union[None, str, List[str]] ) -> Dict[str, TransitionGroup]:
         '''
         Loads the transition group for a given peptide ID and charge across all files
         Args:

diff --git a/massdash/loaders/MzMLDataLoader.py b/massdash/loaders/MzMLDataLoader.py
@@ -34,7 +34,7 @@ def __init__(self, **kwargs):
         if self.libraryAccess is None:
             raise ValueError("If .osw file is not supplied, library file is required for MzMLDataLoader to perform targeted extraction")
 
-    def loadTransitionGroups(self, pep_id: str, charge: int, config: TargetedDIAConfig, runNames: None | str |List[str]=None) -> Dict[str, TransitionGroup]:
+    def loadTransitionGroups(self, pep_id: str, charge: int, config: TargetedDIAConfig, runNames: Union[None, str, List[str]]=None) -> Dict[str, TransitionGroup]:
         '''
         Loads the transition group for a given peptide ID and charge across all files
 
@@ -73,7 +73,7 @@ def loadTransitionGroupsDf(self, pep_id: str, charge: int, config: TargetedDIACo
         out_df = out_df.loc[:,~out_df.columns.duplicated()]
         return out_df
 
-    def loadFeatureMaps(self, pep_id: str, charge: int, config=TargetedDIAConfig, runNames: None | str | List[str] = None) -> FeatureMapCollection:
+    def loadFeatureMaps(self, pep_id: str, charge: int, config=TargetedDIAConfig, runNames: Union[None, str, List[str]] = None) -> FeatureMapCollection:
         '''
         Loads a dictionary of FeatureMaps (where the keys are the filenames) from the results file
 

diff --git a/massdash/loaders/ResultsLoader.py b/massdash/loaders/ResultsLoader.py
@@ -124,7 +124,7 @@ def loadTransitionGroupFeaturesDf(self, pep_id: str, charge: int) -> pd.DataFram
 
         return pd.concat(out).reset_index().drop(columns='level_1').rename(columns=dict(level_0='runname'))
 
-    def loadTransitionGroupFeatures(self, pep_id: str, charge: int, runNames: str | List[str] | None = None) -> TransitionGroupFeatureCollection:
+    def loadTransitionGroupFeatures(self, pep_id: str, charge: int, runNames: Union[str, List[str], None] = None) -> TransitionGroupFeatureCollection:
         """
         Load TransitionGroupFeature objects from the results file for the given peptide precursor
 

diff --git a/massdash/loaders/SqMassLoader.py b/massdash/loaders/SqMassLoader.py
@@ -63,7 +63,7 @@ def loadTransitionGroupsDf(self, pep_id: str, charge: int) -> pd.DataFrame:
 
         return pd.concat(out).reset_index().drop('level_1', axis=1).rename(columns=dict(level_0='run'))
 
-    def loadTransitionGroups(self, pep_id: str, charge: int, runNames: None | str | List[str] =None) -> Dict[str, TransitionGroupCollection]:
+    def loadTransitionGroups(self, pep_id: str, charge: int, runNames: Union[None, str, List[str]] =None) -> Dict[str, TransitionGroupCollection]:
         '''
         Loads the transition group for a given peptide ID and charge across all files
         Args: