Release 1.5.0

Author: jpgill86

doc/examples.rst

@@ -90,3 +90,13 @@ Viewers from Neo objects
 :download:`viewers_with_neo_objects.py <../examples/viewers_with_neo_objects.py>`
 
 .. literalinclude:: ../examples/viewers_with_neo_objects.py
+
+
+Viewers for SpikeInterface objects
+----------------------------------
+
+.. image:: img/viewers_with_spikeinterface_objects.png
+
+:download:`viewers_with_spikeinterface_objects.py <../examples/viewers_with_spikeinterface_objects.py>`
+
+.. literalinclude:: ../examples/viewers_with_spikeinterface_objects.py

doc/img/viewers_with_spikeinterface_objects.png

@@ -4,12 +4,12 @@ Installation
 ============
 
 Requirements:
-  * Python ≥ 3.5
+  * Python ≥ 3.7
   * numpy
   * scipy
   * matplotlib ≥ 2.0
   * pyqtgraph ≥ 0.10.0
-  * PyQt5, PySide2, or PyQt4 (manual installation required)
+  * PyQt5 or PySide2 (manual installation required)
 
 Optional dependencies:
   * Neo ≥ 0.6 (standalone app and Neo sources)

doc/installation.rst

@@ -6,6 +6,7 @@ Release Notes
 .. toctree::
     :maxdepth: 1
 
+    releases/1.5.0.rst
     releases/1.4.0.rst
     releases/1.3.1.rst
     releases/1.3.0.rst

doc/releasenotes.rst

@@ -0,0 +1,33 @@
+Version 1.5.0
+-------------
+
+2021-09-09
+
+Compatibility
+.............
+
+Support for Python < 3.7 and for PyQt4 were dropped.
+
+* Add compatibility with Neo 0.10.0
+  (:pr:`151`, :pr:`157`, :pr:`159`)
+
+* Add PySide2 support
+  (:pr:`148`)
+
+New data sources
+................
+
+* Add data sources for SpikeInterface recording and sorting objects
+  (:pr:`153`)
+
+Continuous integration
+......................
+
+* Run automated test suite with GitHub Actions
+  (:pr:`137`, :pr:`138`, :pr:`142`, :pr:`145`, :pr:`149`)
+
+* Add manually-triggerable GitHub Action workflows for publishing to PyPI
+  (:pr:`140`)
+
+* Add Coveralls test coverage reporting
+  (:pr:`144`)

doc/releases/1.5.0.rst

@@ -77,7 +77,7 @@ def __init__(self, epoch=None, possible_labels=[], color_labels=None, channel_na
         # add labels missing from possible_labels but found in epoch data
         new_labels_from_data = list(set(epoch['label'])-set(self.possible_labels))
         if restrict_to_possible_labels:
-            assert len(new_labels_from_data)==0, 'epoch data contains labels not found in possible_labels: ' + str(new_labels_from_data)
+            assert len(new_labels_from_data)==0, f'epoch data contains labels not found in possible_labels: {new_labels_from_data}'
         self.possible_labels += new_labels_from_data
 
         # put the epochs into a canonical order after loading

ephyviewer/datasource/epochs.py

@@ -1,5 +1,5 @@
 """
-Integrate
+Data sources for SpikeInterface
 """
 
 from .sourcebase import BaseDataSource
@@ -11,9 +11,8 @@
 try:
     from distutils.version import LooseVersion as V
     import spikeinterface
-    if V(spikeinterface.__version__)>='0.90.0':
+    if V(spikeinterface.__version__)>='0.90.1':
         HAVE_SI = True
-        from neo.rawio.baserawio import BaseRawIO
     else:
         HAVE_SI = False
 except ImportError:
@@ -24,10 +23,10 @@
 from .spikes import BaseSpikeSource
 
 
-class FromSpikeinterfaceRecordingSource(BaseAnalogSignalSource):
+class SpikeInterfaceRecordingSource(BaseAnalogSignalSource):
     def __init__(self, recording, segment_index=0):
         BaseAnalogSignalSource.__init__(self)
-        
+
         self.recording = recording
         self.segment_index = segment_index
 
@@ -67,13 +66,13 @@ def index_to_time(self, ind):
 
 
 
-class FromSpikeinterfaceSorintgSource(BaseSpikeSource):
+class SpikeInterfaceSortingSource(BaseSpikeSource):
     def __init__(self, sorting, segment_index=0):
         BaseSpikeSource.__init__(self)
-        
+
         self.sorting = sorting
         self.segment_index = segment_index
-        
+
         #TODO
         self._t_stop = 10.
 

ephyviewer/datasource/spikeinterfacesources.py

@@ -159,13 +159,13 @@ def test_spikeinterface_sources():
     from spikeinterface.core.testing_tools import generate_recording, generate_sorting
 
     recording = generate_recording()
-    source = ephyviewer.FromSpikeinterfaceRecordingSource(recording=recording)
+    source = ephyviewer.SpikeInterfaceRecordingSource(recording=recording)
     print(source)
 
     print(source.t_start, source.nb_channel, source.sample_rate)
 
     sorting = generate_sorting()
-    source = ephyviewer.FromSpikeinterfaceSorintgSource(sorting=sorting)
+    source = ephyviewer.SpikeInterfaceSortingSource(sorting=sorting)
     print(source)
 
     print(source.t_start, source.nb_channel, source.get_channel_name())

ephyviewer/tests/test_datasource.py

@@ -8,11 +8,12 @@ def test_spikeinterface_viewer(interactive=False):
     import spikeinterface as si
     from spikeinterface.core.testing_tools import generate_recording, generate_sorting
 
+
     recording = generate_recording()
-    sig_source = ephyviewer.FromSpikeinterfaceRecordingSource(recording=recording)
+    sig_source = ephyviewer.SpikeInterfaceRecordingSource(recording=recording)
 
     sorting = generate_sorting()
-    spike_source = ephyviewer.FromSpikeinterfaceSorintgSource(sorting=sorting)
+    spike_source = ephyviewer.SpikeInterfaceSortingSource(sorting=sorting)
 
     app = ephyviewer.mkQApp()
     win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)

ephyviewer/tests/test_spikeinterfaceviewer.py

@@ -1 +1 @@
-version = '1.4.1.dev'
+version = '1.5.0'

ephyviewer/version.py

@@ -0,0 +1,43 @@
+"""
+Here is an example of opening viewers directly from spikeinterface objects : recording and sorting.
+
+In this example, recording and sorting are fake ones generated by spikeinterface but of you course 
+you can use any format supported by spikeinterface.
+
+Note that you can display any lazy preprocessor from
+`spikeinterface.toolkit.preprocessing` (filtering, denoising, whittening, ...) so you can see immediatly
+the clean signal.
+
+
+
+"""
+import ephyviewer
+import spikeinterface.full as si
+from spikeinterface.core.testing_tools import generate_recording, generate_sorting
+
+
+recording = generate_recording()
+sig_source = ephyviewer.SpikeInterfaceRecordingSource(recording=recording)
+
+filtered_recording = si.bandpass_filter(recording, freq_min=60., freq_max=100.)
+sig_filtered_source = ephyviewer.SpikeInterfaceRecordingSource(recording=filtered_recording)
+
+sorting = generate_sorting()
+spike_source = ephyviewer.SpikeInterfaceSortingSource(sorting=sorting)
+
+app = ephyviewer.mkQApp()
+win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
+
+view = ephyviewer.TraceViewer(source=sig_source, name='signals')
+win.add_view(view)
+
+view = ephyviewer.TraceViewer(source=sig_filtered_source, name='signals filtered')
+win.add_view(view)
+
+view = ephyviewer.SpikeTrainViewer(source=spike_source, name='spikes')
+win.add_view(view)
+
+
+win.show()
+app.exec_()
+