Merge branch 'master' into fix_edf_handle

h-mayorquin · h-mayorquin · commit ade13db1cc5b · 2024-10-16T10:18:16.000-06:00
diff --git a/neo/io/igorproio.py b/neo/io/igorproio.py
@@ -142,7 +142,7 @@ def _wave_to_analogsignal(self, content, dirpath):
             _time_unit_structure = header["dimUnits"].ravel()
             # For the files we've seen so far, the first element of _time_unit_structure contains the units.
             # If someone has a file for which this assumption does not hold an Exception will be raised.
-            if not all([element == b'' for element in _time_unit_structure[1:]]):
+            if not all([element == b"" for element in _time_unit_structure[1:]]):
                 raise Exception(
                     "Neo cannot yet handle the units in this file. "
                     "Please create a new issue in the Neo issue tracker at "
diff --git a/neo/rawio/axographrawio.py b/neo/rawio/axographrawio.py
@@ -814,7 +814,17 @@ def _scan_axograph_file(self):
                     # channel_info will be cast to _signal_channel_dtype
                     buffer_id = ""
                     stream_id = "0"
-                    channel_info = (name, str(i), 1 / sampling_period, f.byte_order + dtype, units, gain, offset, stream_id, buffer_id)
+                    channel_info = (
+                        name,
+                        str(i),
+                        1 / sampling_period,
+                        f.byte_order + dtype,
+                        units,
+                        gain,
+                        offset,
+                        stream_id,
+                        buffer_id,
+                    )
 
                     self.logger.debug("channel_info: {channel_info}")
                     self.logger.debug("")
diff --git a/neo/rawio/axonrawio.py b/neo/rawio/axonrawio.py
@@ -229,7 +229,9 @@ def _parse_header(self):
                 gain, offset = 1.0, 0.0
             stream_id = "0"
             buffer_id = "0"
-            signal_channels.append((name, str(chan_id), self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+            signal_channels.append(
+                (name, str(chan_id), self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+            )
 
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
diff --git a/neo/rawio/baserawio.py b/neo/rawio/baserawio.py
@@ -94,7 +94,10 @@
 _signal_stream_dtype = [
     ("name", "U64"),  # not necessarily unique
     ("id", "U64"),  # must be unique
-    ("buffer_id", "U64"), # should be "" (empty string) when the stream is not nested under a buffer or the buffer is undefined for some reason.
+    (
+        "buffer_id",
+        "U64",
+    ),  # should be "" (empty string) when the stream is not nested under a buffer or the buffer is undefined for some reason.
 ]
 
 _signal_channel_dtype = [
diff --git a/neo/rawio/brainvisionrawio.py b/neo/rawio/brainvisionrawio.py
@@ -118,7 +118,9 @@ def _parse_header(self):
             offset = 0
             stream_id = "0"
             buffer_id = "0"
-            sig_channels.append((name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+            sig_channels.append(
+                (name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+            )
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
 
         # No spikes
diff --git a/neo/rawio/elanrawio.py b/neo/rawio/elanrawio.py
@@ -158,7 +158,6 @@ def _parse_header(self):
         # unique buffer and stream
         signal_buffers = np.array([("Signals", "0")], dtype=_signal_buffer_dtype)
         signal_streams = np.array([("Signals", "0", "0")], dtype=_signal_stream_dtype)
-        
 
         sig_channels = []
         for c, chan_info in enumerate(channel_infos[:-2]):
@@ -172,7 +171,17 @@ def _parse_header(self):
             stream_id = "0"
             buffer_id = "0"
             sig_channels.append(
-                (chan_name, chan_id, self._sampling_rate, sig_dtype, chan_info["units"], gain, offset, stream_id, buffer_id)
+                (
+                    chan_name,
+                    chan_id,
+                    self._sampling_rate,
+                    sig_dtype,
+                    chan_info["units"],
+                    gain,
+                    offset,
+                    stream_id,
+                    buffer_id,
+                )
             )
 
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
@@ -242,7 +242,6 @@ def _parse_header(self):
 
         stream_ids = np.unique(signal_channels["stream_id"])
         signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
-        
 
         # we need to sort the data because the string of stream_index 10 is mis-sorted.
         buffer_ids = []
diff --git a/neo/rawio/maxwellrawio.py b/neo/rawio/maxwellrawio.py
@@ -111,13 +111,12 @@ def _parse_header(self):
             raise NotImplementedError(f"This version {version} is not supported")
 
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
-        
+
         # one stream per buffer
         signal_buffers = np.zeros(signal_streams.size, dtype=_signal_buffer_dtype)
         signal_buffers["id"] = signal_streams["id"]
         signal_buffers["name"] = signal_streams["name"]
 
-
         # create signal channels
         max_sig_length = 0
         self._signals = {}
@@ -160,7 +159,6 @@ def _parse_header(self):
                     warnings.warn(f"No 'routed' group found for well {stream_id}")
                     well_indices_to_remove.append(stream_index)
                     continue
-                
 
             channel_ids = np.array(mapping["channel"])
             electrode_ids = np.array(mapping["electrode"])
@@ -173,7 +171,9 @@ def _parse_header(self):
                 ch_name = f"ch{chan_id} elec{elec_id}"
                 offset_uV = 0
                 buffer_id = stream_id
-                sig_channels.append((ch_name, str(chan_id), sr, "uint16", "uV", gain_uV, offset_uV, stream_id, buffer_id))
+                sig_channels.append(
+                    (ch_name, str(chan_id), sr, "uint16", "uV", gain_uV, offset_uV, stream_id, buffer_id)
+                )
 
             self._signals[stream_id] = sigs
             max_sig_length = max(max_sig_length, sigs.shape[1])
diff --git a/neo/rawio/micromedrawio.py b/neo/rawio/micromedrawio.py
@@ -130,7 +130,9 @@ def _parse_header(self):
                 chan_id = str(c)
                 stream_id = "0"
                 buffer_id = "0"
-                signal_channels.append((chan_name, chan_id, sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+                signal_channels.append(
+                    (chan_name, chan_id, sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+                )
 
             signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
diff --git a/neo/rawio/neuralynxrawio/neuralynxrawio.py b/neo/rawio/neuralynxrawio/neuralynxrawio.py
@@ -279,7 +279,17 @@ def _parse_header(self):
                         gain *= -1
                     offset = 0.0
                     signal_channels.append(
-                        (chan_name, str(chan_id), info["sampling_rate"], "int16", units, gain, offset, stream_id, buffer_id)
+                        (
+                            chan_name,
+                            str(chan_id),
+                            info["sampling_rate"],
+                            "int16",
+                            units,
+                            gain,
+                            offset,
+                            stream_id,
+                            buffer_id,
+                        )
                     )
                     self.ncs_filenames[chan_uid] = filename
                     keys = [
diff --git a/neo/rawio/neuronexusrawio.py b/neo/rawio/neuronexusrawio.py
@@ -191,7 +191,7 @@ def _parse_header(self):
                     1,  # no gain
                     0,  # no offset
                     stream_id,
-                    buffer_id
+                    buffer_id,
                 )
             )
 
@@ -203,7 +203,7 @@ def _parse_header(self):
         stream_ids = np.unique(signal_channels["stream_id"])
         signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
         signal_streams["id"] = [str(stream_id) for stream_id in stream_ids]
-        # One unique buffer
+        # One unique buffer
         signal_streams["buffer_id"] = buffer_id
 
         for stream_index, stream_id in enumerate(stream_ids):
diff --git a/neo/rawio/neuroscoperawio.py b/neo/rawio/neuroscoperawio.py
@@ -121,7 +121,9 @@ def _parse_header(self):
             offset = 0.0
             stream_id = "0"
             buffer_id = "0"
-            sig_channels.append((name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+            sig_channels.append(
+                (name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+            )
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
 
         # No events
diff --git a/neo/rawio/openephysrawio.py b/neo/rawio/openephysrawio.py
@@ -230,7 +230,7 @@ def _parse_header(self):
             signal_streams = []
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
         # no buffer handling in this format because one channel per file
-        signal_buffers = np.array( [], dtype=_signal_buffer_dtype)
+        signal_buffers = np.array([], dtype=_signal_buffer_dtype)
 
         # scan for spikes files
         spike_channels = []
diff --git a/neo/rawio/plexonrawio.py b/neo/rawio/plexonrawio.py
@@ -272,11 +272,12 @@ def _parse_header(self):
                 )
             offset = 0.0
 
-
             channel_prefix = re.match(regex_prefix_pattern, name).group(0)
             stream_id = channel_prefix
             buffer_id = ""
-            signal_channels.append((name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+            signal_channels.append(
+                (name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+            )
 
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
diff --git a/neo/rawio/rawbinarysignalrawio.py b/neo/rawio/rawbinarysignalrawio.py
@@ -105,7 +105,7 @@ def _parse_header(self):
                         self.signal_gain,
                         self.signal_offset,
                         stream_id,
-                        buffer_id
+                        buffer_id,
                     )
                 )
 
diff --git a/neo/rawio/spike2rawio.py b/neo/rawio/spike2rawio.py
@@ -256,7 +256,9 @@ def _parse_header(self):
                     sig_dtype = "float32"
                 stream_id = "0"  # set it after the loop
                 buffer_id = ""
-                signal_channels.append((name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+                signal_channels.append(
+                    (name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+                )
 
             elif chan_info["kind"] in [2, 3, 4, 5, 8]:
                 # Event
diff --git a/neo/rawio/spikegadgetsrawio.py b/neo/rawio/spikegadgetsrawio.py
@@ -271,7 +271,6 @@ def _parse_header(self):
             self._mask_channels_bytes[stream_id] = mask
             self._mask_streams[stream_id] = np.any(mask, axis=0)
 
-
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
         # no buffer concept here data are too fragmented
diff --git a/neo/rawio/tdtrawio.py b/neo/rawio/tdtrawio.py
@@ -311,7 +311,9 @@ def _parse_header(self):
                 gain = 1.0
                 offset = 0.0
                 buffer_id = ""
-                signal_channels.append((chan_name, str(chan_id), sampling_rate, dtype, units, gain, offset, stream_id, buffer_id))
+                signal_channels.append(
+                    (chan_name, str(chan_id), sampling_rate, dtype, units, gain, offset, stream_id, buffer_id)
+                )
 
         if missing_sev_channels:
             warnings.warn(f"Could not identify sev files for channels {missing_sev_channels}.")
diff --git a/neo/rawio/winedrrawio.py b/neo/rawio/winedrrawio.py
@@ -94,7 +94,9 @@ def _parse_header(self):
             offset = -YZ * gain
             stream_id = "0"
             buffer_id = "0"
-            signal_channels.append((name, str(chan_id), self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id))
+            signal_channels.append(
+                (name, str(chan_id), self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id)
+            )
 
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
@@ -104,7 +106,7 @@ def _parse_header(self):
         for i in range(unique_characteristics.size):
             mask = unique_characteristics[i] == characteristics
             signal_channels["stream_id"][mask] = str(i)
-            # unique buffer for all streams    
+            # unique buffer for all streams
             buffer_id = "0"
             signal_streams.append((f"stream {i}", str(i), buffer_id))
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
diff --git a/neo/rawio/winwcprawio.py b/neo/rawio/winwcprawio.py
@@ -119,7 +119,9 @@ def _parse_header(self):
             offset = 0.0
             stream_id = "0"
             buffer_id = "0"
-            signal_channels.append((name, chan_id, self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id))
+            signal_channels.append(
+                (name, chan_id, self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id)
+            )
 
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
@@ -129,7 +131,7 @@ def _parse_header(self):
         for i in range(unique_characteristics.size):
             mask = unique_characteristics[i] == characteristics
             signal_channels["stream_id"][mask] = str(i)
-            # unique buffer for all streams    
+            # unique buffer for all streams
             buffer_id = "0"
             signal_streams.append((f"stream {i}", str(i), buffer_id))
         signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
diff --git a/neo/test/rawiotest/rawio_compliance.py b/neo/test/rawiotest/rawio_compliance.py
@@ -78,6 +78,7 @@ def header_is_total(reader):
         for k, _ in _event_channel_dtype:
             assert k in dt.fields, f"{k} not in event_channels.dtype"
 
+
 def check_signal_stream_buffer_hierachy(reader):
     # rules:
     #  * a channel always belong to a stream
@@ -95,7 +96,7 @@ def check_signal_stream_buffer_hierachy(reader):
         assert channel["stream_id"] in h["signal_streams"]["id"]
         if channel["buffer_id"] != "":
             assert channel["buffer_id"] in h["signal_buffers"]["id"]
-    
+
     stream_ids = h["signal_streams"]["id"]
     if stream_ids.size > 0:
         assert stream_ids.size == np.unique(stream_ids).size
diff --git a/neo/test/rawiotest/test_neuronexusrawio.py b/neo/test/rawiotest/test_neuronexusrawio.py
@@ -15,4 +15,4 @@ class TestNeuroNexusRawIO(
 
 
 if __name__ == "__main__":
-    unittest.main()
+    unittest.main()
diff --git a/pyproject.toml b/pyproject.toml
@@ -45,7 +45,7 @@ iocache = [
 ]
 
 test = [
-    "dhn_med_py>=1.0.0",
+    "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
     "pytest",
     "pytest-cov",
     # datalad   # this dependency is covered by conda (environment_testing.yml)
@@ -100,13 +100,13 @@ ced = ["sonpy"]
 nwb = ["pynwb"]
 maxwell = ["h5py"]
 biocam = ["h5py"]
-med = ["dhn_med_py>=1.0.0"]
+med = ["dhn_med_py<2.0"] # ci failing with 2.0 test future version when stable
 plexon2 = ["zugbruecke>=0.2; sys_platform!='win32'", "wenv; sys_platform!='win32'"]
 
 all = [
     "coverage",
     "coveralls",
-    "dhn_med_py>=1.0.0",
+    "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
     "h5py",
     "igor2",
     "ipython",
