Fix RTD examples

LorenFrankLab · Nov 19, 2021 · 9428cfc · 9428cfc
1 parent 0f9c30d
commit 9428cfc
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Showing 5 changed files with 8 additions and 7 deletions.
diff --git a/examples/getting_started/plot_getting_started.py b/examples/getting_started/plot_getting_started.py
@@ -175,7 +175,7 @@
 
 we_TDC = si.WaveformExtractor.create(recording_preprocessed, sorting_TDC, 'waveforms', remove_if_exists=True)
 we_TDC.set_params(ms_before=3., ms_after=4., max_spikes_per_unit=500)
-we_TDC.run(n_jobs=-1, chunk_size=30000)
+we_TDC.run_extract_waveforms(n_jobs=-1, chunk_size=30000)
 print(we_TDC)
 
 unit_id0 = sorting_TDC.unit_ids[0]

diff --git a/examples/modules/sorters/plot_1_sorters_example.py b/examples/modules/sorters/plot_1_sorters_example.py
@@ -46,18 +46,18 @@
 default_TDC_params['detect_threshold'] = 5
 
 # parameters set by params dictionary
-sorting_TDC = ss.run_tridesclous(recording=recording, output_folder='tmp_TDC_5',
+sorting_TDC_5 = ss.run_tridesclous(recording=recording, output_folder='tmp_TDC_5',
                                    **default_TDC_params, )
 ##############################################################################
 
 # parameters set by params dictionary
 sorting_TDC_8 = ss.run_tridesclous(recording=recording, output_folder='tmp_TDC_8',
-                            detect_threshold=8.)
+                                   detect_threshold=8.)
 
 
 ##############################################################################
 
-print('Units found with threshold = 4:', sorting_TDC.get_unit_ids())
+print('Units found with threshold = 5:', sorting_TDC_5.get_unit_ids())
 print('Units found with threshold = 8:', sorting_TDC_8.get_unit_ids())
 
 ##############################################################################

diff --git a/examples/modules/sorters/plot_4_sorting_concatenated_recordings.py b/examples/modules/sorters/plot_4_sorting_concatenated_recordings.py
@@ -28,7 +28,7 @@
 # Let's create a toy example with 4 channels (the :code:`dumpable=True` dumps the extractors to a file, which is
 # required for parallel sorting):
 
-recording_single, _ = si.toy_example(duration=10, num_channels=4, dumpable=True, num_segments=1)
+recording_single, _ = si.toy_example(duration=10, num_channels=4, seed=0, num_segments=1)
 print(recording_single)
 
 # make dumpable

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-numpy<=1.20
+numpy<1.21
 neo>=0.10.0
 joblib
 tqdm

diff --git a/spikeinterface/core/waveform_extractor.py b/spikeinterface/core/waveform_extractor.py
@@ -227,7 +227,8 @@ def get_waveforms(self, unit_id, with_index=False, sparsity=None):
         if wfs is None:
             waveform_file = self.folder / 'waveforms' / f'waveforms_{unit_id}.npy'
             if not waveform_file.is_file():
-                raise Exception('waveforms not extracted yet : please do WaveformExtractor.run_extract_waveforms() fisrt')
+                raise Exception('Waveforms not extracted yet: '
+                                'please do WaveformExtractor.run_extract_waveforms() first')
 
             wfs = np.load(waveform_file)
             self._waveforms[unit_id] = wfs