fix merge issues

sed/core/processor.py

@@ -285,8 +285,7 @@ def load(
         if metadata is None:
             metadata = {}
         if dataframe is not None:
-            self._dataframe = dataframe
-            self._timed_dataframe = None
+            timed_dataframe = kwds.pop("timed_dataframe", None)
         elif runs is not None:
             # If runs are provided, we only use the copy tool if also folder is provided.
             # In that case, we copy the whole provided base folder tree, and pass the copied
@@ -314,15 +313,13 @@ def load(
                 collect_metadata=collect_metadata,
                 **kwds,
             )
-
         elif files is not None:
             dataframe, timed_dataframe, metadata = self.loader.read_dataframe(
                 files=cast(List[str], self.cpy(files)),
                 metadata=metadata,
                 collect_metadata=collect_metadata,
                 **kwds,
             )
-
         else:
             raise ValueError(
                 "Either 'dataframe', 'files', 'folder', or 'runs' needs to be provided!",
@@ -1417,11 +1414,9 @@ def compute(
                 print(
                     f"Calculate normalization histogram for axis '{axis}'...",
                 )
-                self._normalization_histogram = (
-                    self.get_normalization_histogram(
-                        axis=axis,
-                        df_partitions=df_partitions,
-                    )
+                self._normalization_histogram = self.get_normalization_histogram(
+                    axis=axis,
+                    df_partitions=df_partitions,
                 )
                 # if the axes are named correctly, xarray figures out the normalization correctly
                 self._normalized = self._binned / self._normalization_histogram
@@ -1443,9 +1438,7 @@ def compute(
                 )
 
             self._normalized.attrs["units"] = "counts/second"
-            self._normalized.attrs[
-                "long_name"
-            ] = "photoelectron counts per second"
+            self._normalized.attrs["long_name"] = "photoelectron counts per second"
             self._normalized.attrs["metadata"] = self._attributes.metadata
 
             return self._normalized
@@ -1496,41 +1489,33 @@ def get_normalization_histogram(
 
         if use_time_stamps or self._timed_dataframe is None:
             if df_partitions is not None:
-                self._normalization_histogram = (
-                    normalization_histogram_from_timestamps(
-                        self._dataframe.partitions[df_partitions],
-                        axis,
-                        self._binned.coords[axis].values,
-                        self._config["dataframe"]["time_stamp_alias"],
-                    )
+                self._normalization_histogram = normalization_histogram_from_timestamps(
+                    self._dataframe.partitions[df_partitions],
+                    axis,
+                    self._binned.coords[axis].values,
+                    self._config["dataframe"]["time_stamp_alias"],
                 )
             else:
-                self._normalization_histogram = (
-                    normalization_histogram_from_timestamps(
-                        self._dataframe,
-                        axis,
-                        self._binned.coords[axis].values,
-                        self._config["dataframe"]["time_stamp_alias"],
-                    )
+                self._normalization_histogram = normalization_histogram_from_timestamps(
+                    self._dataframe,
+                    axis,
+                    self._binned.coords[axis].values,
+                    self._config["dataframe"]["time_stamp_alias"],
                 )
         else:
             if df_partitions is not None:
-                self._normalization_histogram = (
-                    normalization_histogram_from_timed_dataframe(
-                        self._timed_dataframe.partitions[df_partitions],
-                        axis,
-                        self._binned.coords[axis].values,
-                        self._config["dataframe"]["timed_dataframe_unit_time"],
-                    )
+                self._normalization_histogram = normalization_histogram_from_timed_dataframe(
+                    self._timed_dataframe.partitions[df_partitions],
+                    axis,
+                    self._binned.coords[axis].values,
+                    self._config["dataframe"]["timed_dataframe_unit_time"],
                 )
             else:
-                self._normalization_histogram = (
-                    normalization_histogram_from_timed_dataframe(
-                        self._timed_dataframe,
-                        axis,
-                        self._binned.coords[axis].values,
-                        self._config["dataframe"]["timed_dataframe_unit_time"],
-                    )
+                self._normalization_histogram = normalization_histogram_from_timed_dataframe(
+                    self._timed_dataframe,
+                    axis,
+                    self._binned.coords[axis].values,
+                    self._config["dataframe"]["timed_dataframe_unit_time"],
                 )
 
         return self._normalization_histogram

sed/loader/base/loader.py

@@ -147,28 +147,6 @@ def get_files_from_run_id(
         """
         raise NotImplementedError
 
-    @abstractmethod
-    def get_files_from_run_id(
-        self,
-        run_id: str,
-        folders: Union[str, Sequence[str]] = None,
-        extension: str = None,
-        **kwds,
-    ) -> List[str]:
-        """Locate the files for a given run identifier.
-
-        Args:
-            run_id (str): The run identifier to locate.
-            folders (Union[str, Sequence[str]], optional): The directory(ies) where the raw
-                data is located. Defaults to None.
-            extension (str, optional): The file extension. Defaults to None.
-            kwds: Keyword arguments
-
-        Return:
-            List[str]: List of files for the given run.
-        """
-        raise NotImplementedError
-
     @abstractmethod
     def get_count_rate(
         self,

sed/loader/flash/loader.py

@@ -595,7 +595,7 @@ def read_dataframe(
         metadata: dict = None,
         collect_metadata: bool = False,
         **kwds,
-    ) -> Tuple[dd.DataFrame, dict]:
+    ) -> Tuple[dd.DataFrame, dd.DataFrame, dict]:
         """
         Read express data from the DAQ, generating a parquet in between.
 
@@ -712,7 +712,7 @@ def read_dataframe(
 
         metadata = self.parse_metadata() if collect_metadata else {}
 
-        return dataframe, metadata
+        return dataframe, None, metadata
 
     def get_files_from_run_id(
         self,

tests/calibrator/test_energy.py

@@ -258,7 +258,7 @@ def test_append_energy_axis_raises():
     """Test if apply_correction raises the correct errors"""
     config = parse_config(config={}, folder_config={}, user_config={}, system_config={})
     loader = get_loader(loader_name="mpes", config=config)
-    df, _ = loader.read_dataframe(folders=df_folder, collect_metadata=False)
+    df, _, _ = loader.read_dataframe(folders=df_folder, collect_metadata=False)
     ec = EnergyCalibrator(config=config, loader=loader)
     with pytest.raises(ValueError):
         df, _ = ec.append_energy_axis(df, calibration={"d": 1, "t0": 0})

tests/test_diagnostics.py

@@ -31,7 +31,7 @@ def test_plot_histogram(ncols: int, backend: str):
         ncols (int): number of columns
         backend (str): plotting backend to use
     """
-    dataframe, _ = loader.read_dataframe(files=files)
+    dataframe, _, _ = loader.read_dataframe(files=files)
     axes = config["histogram"]["axes"]
     ranges = config["histogram"]["ranges"]
     bins = config["histogram"]["bins"]

tests/test_processor.py

@@ -48,7 +48,7 @@
 def test_processor_from_dataframe():
     """Test generation of the processor from a dataframe object"""
     config = {"core": {"loader": "generic"}}
-    dataframe, _ = loader.read_dataframe(files=files)
+    dataframe, _, _ = loader.read_dataframe(files=files)
     processor = SedProcessor(
         dataframe=dataframe,
         config=config,
@@ -63,7 +63,7 @@ def test_processor_from_dataframe():
 def test_processor_from_files():
     """Test generation of the processor from a list of files"""
     config = {"core": {"loader": "generic"}}
-    dataframe, _ = loader.read_dataframe(files=files)
+    dataframe, _, _ = loader.read_dataframe(files=files)
     processor = SedProcessor(
         files=files,
         config=config,
@@ -78,7 +78,7 @@ def test_processor_from_files():
 def test_processor_from_folders():
     """Test generation of the processor from a folder"""
     config = {"core": {"loader": "generic"}}
-    dataframe, _ = loader.read_dataframe(files=files)
+    dataframe, _, _ = loader.read_dataframe(files=files)
     processor = SedProcessor(
         folder=df_folder,
         config=config,