Merge branch 'main' of https://github.com/datajoint/workflow-array-ephys

 into main

requirements.txt

@@ -1,6 +1,7 @@
 datajoint>=0.13.0
-element-array-ephys
-element-lab
-element-animal
+element-array-ephys 
+element-lab 
+element-animal 
 element-session
+element-data-loader @ git+https://github.com/datajoint/element-data-loader.git
 ipykernel

tests/__init__.py

@@ -13,7 +13,7 @@
 
 # ------------------- SOME CONSTANTS -------------------
 
-_tear_down = False
+_tear_down = True
 
 test_user_data_dir = pathlib.Path('./tests/user_data')
 test_user_data_dir.mkdir(exist_ok=True)

workflow_array_ephys/ingest.py

@@ -35,9 +35,9 @@ def ingest_sessions(session_csv_path='./user_data/sessions.csv'):
         session_datetimes, insertions = [], []
 
         # search session dir and determine acquisition software
-        for ephys_pattern, ephys_acq_type in zip(['*.ap.meta', '*.oebin'], ['SpikeGLX', 'Open Ephys']):
-            ephys_meta_filepaths = [fp for fp in sess_dir.rglob(ephys_pattern)]
-            if len(ephys_meta_filepaths):
+        for ephys_pattern, ephys_acq_type in zip(['*.ap.meta', '*.oebin'], ['SpikeGLX', 'OpenEphys']):
+            ephys_meta_filepaths = list(session_dir.rglob(ephys_pattern))
+            if ephys_meta_filepaths:
                 acq_software = ephys_acq_type
                 break
         else:
@@ -57,8 +57,8 @@ def ingest_sessions(session_csv_path='./user_data/sessions.csv'):
 
                 insertions.append({'probe': spikeglx_meta.probe_SN, 'insertion_number': int(probe_number)})
                 session_datetimes.append(spikeglx_meta.recording_time)
-        elif acq_software == 'Open Ephys':
-            loaded_oe = openephys.OpenEphys(sess_dir)
+        elif acq_software == 'OpenEphys':
+            loaded_oe = openephys.OpenEphys(session_dir)
             session_datetimes.append(loaded_oe.experiment.datetime)
             for probe_idx, oe_probe in enumerate(loaded_oe.probes.values()):
                 probe_key = {'probe_type': oe_probe.probe_model, 'probe': oe_probe.probe_SN}