Merge pull request #2677 from alejoe91/preprare_0.100.5

Preprare 0.100.5
SpikeInterface · Apr 6, 2024 · 7c2656c · 7c2656c
2 parents 7d0e1da + bb88a49
commit 7c2656c
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Showing 8 changed files with 32 additions and 11 deletions.
diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
@@ -5,6 +5,7 @@ on:
     types: [synchronize, opened, reopened]
     branches:
       - main
+      - 0.100-bug-fixes
 
 concurrency:  # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}

diff --git a/.github/workflows/full-test.yml b/.github/workflows/full-test.yml
@@ -5,6 +5,7 @@ on:
     types: [synchronize, opened, reopened]
     branches:
       - main
+      - 0.100-bug-fixes
 
 concurrency:  # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}

diff --git a/doc/releases/0.100.5.rst b/doc/releases/0.100.5.rst
@@ -0,0 +1,12 @@
+.. _release0.100.5:
+
+SpikeInterface 0.100.5 release notes
+------------------------------------
+
+6th April 2024
+
+Minor release with bug fixes
+
+* Open Ephys: Use discovered recording ids to load sync timestamps (#2655)
+* Fix channel gains in NwbRecordingExtractor with backend (#2661)
+* Fix depth location in spikes on traces map (#2676)
diff --git a/doc/whatisnew.rst b/doc/whatisnew.rst
@@ -8,6 +8,7 @@ Release notes
 .. toctree::
   :maxdepth: 1
 
+  releases/0.100.5.rst
   releases/0.100.4.rst
   releases/0.100.3.rst
   releases/0.100.2.rst
@@ -38,6 +39,11 @@ Release notes
   releases/0.9.1.rst
 
 
+Version 0.100.5
+===============
+
+* Minor release with bug fixes
+
 Version 0.100.4
 ===============
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.100.4"
+version = "0.100.5"
 authors = [
   { name="Alessio Buccino", email="[email protected]" },
   { name="Samuel Garcia", email="[email protected]" },
@@ -59,7 +59,7 @@ changelog = "https://spikeinterface.readthedocs.io/en/latest/whatisnew.html"
 
 extractors = [
     "MEArec>=1.8",
-    "pynwb>=2.3.0",
+    "pynwb>=2.6.0",
     "hdmf-zarr>=0.5.0",
     "pyedflib>=0.1.30",
     "sonpy;python_version<'3.10'",
@@ -80,7 +80,7 @@ streaming_extractors = [
     "fsspec",
     "aiohttp",
     "requests",
-    "pynwb>=2.3.0",
+    "pynwb>=2.6.0",
     "hdmf-zarr>=0.5.0",
     "remfile",
     "s3fs"

diff --git a/src/spikeinterface/extractors/neoextractors/openephys.py b/src/spikeinterface/extractors/neoextractors/openephys.py
@@ -180,6 +180,9 @@ def __init__(
             exp_id = exp_ids[0]
         else:
             exp_id = exp_ids[block_index]
+        rec_ids = sorted(
+            list(self.neo_reader.folder_structure[record_node]["experiments"][exp_id]["recordings"].keys())
+        )
 
         # do not load probe for NIDQ stream or if load_sync_channel is True
         if "NI-DAQmx" not in stream_name and not load_sync_channel:
@@ -229,10 +232,8 @@ def __init__(
         # load synchronized timestamps and set_times to recording
         recording_folder = Path(folder_path) / record_node
         stream_folders = []
-        for segment_index in range(self.get_num_segments()):
-            stream_folder = (
-                recording_folder / f"experiment{exp_id}" / f"recording{segment_index+1}" / "continuous" / oe_stream
-            )
+        for segment_index, rec_id in enumerate(rec_ids):
+            stream_folder = recording_folder / f"experiment{exp_id}" / f"recording{rec_id}" / "continuous" / oe_stream
             stream_folders.append(stream_folder)
             if load_sync_timestamps:
                 if (stream_folder / "sample_numbers.npy").is_file():
@@ -245,7 +246,7 @@ def __init__(
                     sync_times = None
                 try:
                     self.set_times(times=sync_times, segment_index=segment_index, with_warning=False)
-                except AssertionError:
+                except:
                     warnings.warn(f"Could not load synchronized timestamps for {stream_name}")
 
         self._stream_folders = stream_folders

diff --git a/src/spikeinterface/extractors/nwbextractors.py b/src/spikeinterface/extractors/nwbextractors.py
@@ -842,7 +842,8 @@ def _fetch_main_properties_backend(self):
         data_attributes = self.electrical_series["data"].attrs
         electrical_series_conversion = data_attributes["conversion"]
         gains = electrical_series_conversion * 1e6
-        if "channel_conversion" in data_attributes:
+        channel_conversion = self.electrical_series.get("channel_conversion", None)
+        if channel_conversion:
             gains *= self.electrical_series["channel_conversion"][:]
 
         # Channel offsets

diff --git a/src/spikeinterface/widgets/spikes_on_traces.py b/src/spikeinterface/widgets/spikes_on_traces.py
@@ -183,8 +183,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
                 spike_times_to_plot = sorting.get_unit_spike_train(
                     unit, segment_index=segment_index, return_times=True
                 )[spike_start:spike_end]
-                unit_y_loc = min_y + max_y - dp.unit_locations[unit][1]
-                # markers = np.ones_like(spike_frames_to_plot) * (min_y + max_y - dp.unit_locations[unit][1])
+                unit_y_loc = dp.unit_locations[unit][1]
                 width = 2 * 1e-3
                 ellipse_kwargs = dict(width=width, height=10, fc="none", ec=dp.unit_colors[unit], lw=2)
                 patches = [Ellipse((s, unit_y_loc), **ellipse_kwargs) for s in spike_times_to_plot]