ipfx: Avoid using deprecated pynwb interfaces

This fixes the following warnings:

  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/pynwb/base.py:87: DeprecationWarning: get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.
    warn('get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.', DeprecationWarning)

tests/test_mies_nwb_pipeline_output.py: 127 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/pynwb/base.py:82: DeprecationWarning: add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.
    warn('add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.', DeprecationWarning)

Author: t-b

ipfx/dataset/ephys_nwb_data.py

@@ -308,7 +308,7 @@ def get_clamp_mode(self,sweep_number):
 
     def get_spike_times(self, sweep_number):
         spikes = self.nwb.get_processing_module('spikes')
-        sweep_spikes = spikes.get_data_interface(f"Sweep_{sweep_number}")
+        sweep_spikes = spikes.get(f"Sweep_{sweep_number}")
         return sweep_spikes.timestamps
 
     @staticmethod

ipfx/nwb_append.py

@@ -59,7 +59,7 @@ def append_spike_times(input_nwb_path: PathLike,
                             unit='seconds',
                             data=wrapped_spike_times,
                             name=f"Sweep_{sweep_num}")
-            spike_module.add_data_interface(ts)
+            spike_module.add(ts)
 
         nwbfile.add_processing_module(spike_module)
 

tests/test_append_nwb.py

@@ -51,5 +51,5 @@ def test_embed_spike_times_into_nwb(tmpdir_factory):
 
         spikes = nwbfile.get_processing_module('spikes')
         for sweep_num, spike_times in sweep_spike_times.items():
-            sweep_spikes = spikes.get_data_interface(f"Sweep_{sweep_num}").timestamps
+            sweep_spikes = spikes.get(f"Sweep_{sweep_num}").timestamps
             assert np.allclose(sweep_spikes, spike_times)