Merge branch 'main' into add_template_data_class

doc/how_to/load_matlab_data.rst

@@ -30,7 +30,7 @@ Here, we present a MATLAB code that creates a random dataset and writes it to a
 Loading Data in SpikeInterface
 ------------------------------
 
-After executing the above MATLAB code, a binary file named `your_data_as_a_binary.bin` will be created in your MATLAB directory. To load this file in Python, you'll need its full path.
+After executing the above MATLAB code, a binary file named :code:`your_data_as_a_binary.bin` will be created in your MATLAB directory. To load this file in Python, you'll need its full path.
 
 Use the following Python script to load the binary data into SpikeInterface:
 
@@ -55,7 +55,7 @@ Use the following Python script to load the binary data into SpikeInterface:
 
    # Load data using SpikeInterface
    recording = si.read_binary(file_path, sampling_frequency=sampling_frequency,
-                                        num_channels=num_channels, dtype=dtype)
+                              num_channels=num_channels, dtype=dtype)
 
    # Confirm that the data was loaded correctly by comparing the data shapes and see they match the MATLAB data
    print(recording.get_num_frames(), recording.get_num_channels())
@@ -65,18 +65,18 @@ Follow the steps above to seamlessly import your MATLAB data into SpikeInterface
 Common Pitfalls & Tips
 ----------------------
 
-1. **Data Shape**: Make sure your MATLAB data matrix's first dimension is samples/time and the second is channels. If your time is in the second dimension, use `time_axis=1` in `si.read_binary()`.
+1. **Data Shape**: Make sure your MATLAB data matrix's first dimension is samples/time and the second is channels. If your time is in the second dimension, use :code:`time_axis=1` in :code:`si.read_binary()`.
 2. **File Path**: Always double-check the Python file path.
 3. **Data Type Consistency**: Ensure data types between MATLAB and Python are consistent. MATLAB's `double` is equivalent to Numpy's `float64`.
 4. **Sampling Frequency**: Set the appropriate sampling frequency in Hz for SpikeInterface.
-5. **Transition to Python**: Moving from MATLAB to Python can be challenging. For newcomers to Python, consider reviewing numpy's [Numpy for MATLAB Users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) guide.
+5. **Transition to Python**: Moving from MATLAB to Python can be challenging. For newcomers to Python, consider reviewing numpy's `Numpy for MATLAB Users <https://numpy.org/doc/stable/user/numpy-for-matlab-users.html>`_ guide.
 
 Using gains and offsets for integer data
 ----------------------------------------
 
 Raw data formats often store data as integer values for memory efficiency. To give these integers meaningful physical units, you can apply a gain and an offset.
-In SpikeInterface, you can use the `gain_to_uV` and `offset_to_uV` parameters, since traces are handled in microvolts (uV). Both parameters can be integrated into the `read_binary` function.
-If your data in MATLAB is stored as `int16`, and you know the gain and offset, you can use the following code to load the data:
+In SpikeInterface, you can use the :code:`gain_to_uV` and :code:`offset_to_uV` parameters, since traces are handled in microvolts (uV). Both parameters can be integrated into the :code:`read_binary` function.
+If your data in MATLAB is stored as :code:`int16`, and you know the gain and offset, you can use the following code to load the data:
 
 .. code-block:: python
 
@@ -90,7 +90,8 @@ If your data in MATLAB is stored as `int16`, and you know the gain and offset, y
                               num_channels=num_channels, dtype=dtype_int,
                               gain_to_uV=gain_to_uV, offset_to_uV=offset_to_uV)
 
-   recording.get_traces(return_scaled=True)  # Return traces in micro volts (uV)
+   recording.get_traces()  # Return traces in original units [type: int]
+   recording.get_traces(return_scaled=True)  # Return traces in micro volts (uV) [type: float]
 
 
 This will equip your recording object with capabilities to convert the data to float values in uV using the :code:`get_traces()` method with the :code:`return_scaled` parameter set to :code:`True`.

src/spikeinterface/extractors/cellexplorersortingextractor.py

@@ -40,7 +40,6 @@ def __init__(
         sampling_frequency: float | None = None,
         session_info_file_path: str | Path | None = None,
         spikes_matfile_path: str | Path | None = None,
-        session_info_matfile_path: str | Path | None = None,
     ):
         try:
             from pymatreader import read_mat
@@ -67,26 +66,6 @@ def __init__(
                 )
             file_path = spikes_matfile_path if file_path is None else file_path
 
-        if session_info_matfile_path is not None:
-            # Raise an error if the warning period has expired
-            deprecation_issued = datetime.datetime(2023, 4, 1)
-            deprecation_deadline = deprecation_issued + datetime.timedelta(days=180)
-            if datetime.datetime.now() > deprecation_deadline:
-                raise ValueError(
-                    "The session_info_matfile_path argument is no longer supported in. Use session_info_file_path instead."
-                )
-
-            # Otherwise, issue a DeprecationWarning
-            else:
-                warnings.warn(
-                    "The session_info_matfile_path argument is deprecated and will be removed in six months. "
-                    "Use session_info_file_path instead.",
-                    DeprecationWarning,
-                )
-            session_info_file_path = (
-                session_info_matfile_path if session_info_file_path is None else session_info_file_path
-            )
-
         self.spikes_cellinfo_path = Path(file_path)
         self.session_path = self.spikes_cellinfo_path.parent
         self.session_id = self.spikes_cellinfo_path.stem.split(".")[0]

src/spikeinterface/extractors/tests/test_cellexplorerextractor.py

@@ -26,7 +26,7 @@ class CellExplorerSortingTest(SortingCommonTestSuite, unittest.TestCase):
         (
             "cellexplorer/dataset_2/20170504_396um_0um_merge.spikes.cellinfo.mat",
             {
-                "session_info_matfile_path": local_folder
+                "session_info_file_path": local_folder
                 / "cellexplorer/dataset_2/20170504_396um_0um_merge.sessionInfo.mat"
             },
         ),