Merge branch 'master' into release-14.2

zm711 · web-flow · commit 5d5a92039add · 2025-07-08T06:35:56.000-04:00
diff --git a/.github/workflows/plexon2-testing.yml b/.github/workflows/plexon2-testing.yml
@@ -2,17 +2,18 @@ name: NeoPlexon2Test
 
 on:
   workflow_dispatch:
-    schedule:
-      - cron: "0 12 * * 0" # weekly at noon UTC on Sundays
+  schedule:
+    - cron: "0 12 * * 0" # weekly at noon UTC on Sundays
 
 
 jobs:
   build-and-test:
-    name: Test on (${{ inputs.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }})
-    runs-on: ${{ inputs.os }}
+    name: Test on (${{ matrix.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }})
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: true
       matrix:
+        os:  [ubuntu-latest]
         python-version: ['3.9', '3.12']
         numpy-version: ['1.26', '2.0']
     defaults:
diff --git a/neo/rawio/neuralynxrawio/ncssections.py b/neo/rawio/neuralynxrawio/ncssections.py
@@ -51,6 +51,7 @@ class AcqType(IntEnum):
     ATLAS = auto()
     UNKNOWN = auto()
 
+
 class NcsSections:
     """
     Contains information regarding the contiguous sections of records in an Ncs file.
@@ -279,8 +280,13 @@ def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None, strict_gap_mode=Tru
             ncsSects.sampFreqUsed = sampFreqUsed
             ncsSects.microsPerSampUsed = microsPerSampUsed
 
-        elif acqType in [AcqType.DIGITALLYNX, AcqType.DIGITALLYNXSX, AcqType.CHEETAH64,
-                          AcqType.CHEETAH560, AcqType.RAWDATAFILE]:
+        elif acqType in [
+            AcqType.DIGITALLYNX,
+            AcqType.DIGITALLYNXSX,
+            AcqType.CHEETAH64,
+            AcqType.CHEETAH560,
+            AcqType.RAWDATAFILE,
+        ]:
             # digital lynx style with fractional frequency and micros per samp determined from block times
             if gapTolerance is None:
                 if strict_gap_mode:
diff --git a/neo/rawio/neuralynxrawio/nlxheader.py b/neo/rawio/neuralynxrawio/nlxheader.py
@@ -84,11 +84,13 @@ def _to_bool(txt):
     #
     # There are now separate patterns for the in header line and in properties cases which cover
     # the known variations in each case. They are compiled here once for efficiency.
-    _openDatetime1_pat = re.compile(r"## (Time|Date) Opened:* \((m/d/y|mm/dd/yyy)\): (?P<date>\S+)"\
-                                      r"\s+(\(h:m:s\.ms\)|At Time:) (?P<time>\S+)")
+    _openDatetime1_pat = re.compile(
+        r"## (Time|Date) Opened:* \((m/d/y|mm/dd/yyy)\): (?P<date>\S+)" r"\s+(\(h:m:s\.ms\)|At Time:) (?P<time>\S+)"
+    )
     _openDatetime2_pat = re.compile(r"-TimeCreated (?P<date>\S+) (?P<time>\S+)")
-    _closeDatetime1_pat = re.compile(r"## (Time|Date) Closed:* \((m/d/y|mm/dd/yyy)\): " \
-                                        r"(?P<date>\S+)\s+(\(h:m:s\.ms\)|At Time:) (?P<time>\S+)")
+    _closeDatetime1_pat = re.compile(
+        r"## (Time|Date) Closed:* \((m/d/y|mm/dd/yyy)\): " r"(?P<date>\S+)\s+(\(h:m:s\.ms\)|At Time:) (?P<time>\S+)"
+    )
     _closeDatetime2_pat = re.compile(r"-TimeClosed (?P<date>\S+) (?P<time>\S+)")
 
     # Precompiled filename pattern
@@ -287,8 +289,9 @@ def _setBitToMicroVolt(self):
             if len(btm_entries) == 1:
                 btm_entries = btm_entries * len(self["channel_ids"])
             self["bit_to_microVolt"] = [float(e) * 1e6 for e in btm_entries]
-            assert len(self["bit_to_microVolt"]) == len( self["channel_ids"]), \
-                "Number of channel ids does not match bit_to_microVolt conversion factors."
+            assert len(self["bit_to_microVolt"]) == len(
+                self["channel_ids"]
+            ), "Number of channel ids does not match bit_to_microVolt conversion factors."
 
     def _setInputRanges(self, numChidEntries):
         if "InputRange" in self:
@@ -297,44 +300,48 @@ def _setInputRanges(self, numChidEntries):
                 self["InputRange"] = [int(ir_entries[0])] * numChidEntries
             else:
                 self["InputRange"] = [int(e) for e in ir_entries]
-            assert len(self["InputRange"]) == numChidEntries, \
-                "Number of channel ids does not match input range values."
+            assert len(self["InputRange"]) == numChidEntries, "Number of channel ids does not match input range values."
 
     def _setFilenameProp(self, txt_header):
         """
         Add an OriginalFileName property if in header.
         """
-        if not 'OriginalFileName' in self.keys():
+        if not "OriginalFileName" in self.keys():
             fnm = NlxHeader._filename_pat.search(txt_header)
-            if not fnm: return
-            else: self['OriginalFileName'] = fnm.group(1).strip(' "\t\r\n')
+            if not fnm:
+                return
+            else:
+                self["OriginalFileName"] = fnm.group(1).strip(' "\t\r\n')
         else:
             # some file types quote the property so strip that also
-            self['OriginalFileName'] = self['OriginalFileName'].strip(' "\t\r\n')
+            self["OriginalFileName"] = self["OriginalFileName"].strip(' "\t\r\n')
 
     def _setTimeDate(self, txt_header):
         """
         Read time and date from text of header
         """
         import dateutil
+
         # opening time
         sr = NlxHeader._openDatetime1_pat.search(txt_header)
-        if not sr: sr=NlxHeader._openDatetime2_pat.search(txt_header)
+        if not sr:
+            sr = NlxHeader._openDatetime2_pat.search(txt_header)
         if not sr:
             raise IOError(
-                f"No matching header open date/time for application {self['ApplicationName']} " +
-                f"version {self['ApplicationVersion']}. Please contact developers."
+                f"No matching header open date/time for application {self['ApplicationName']} "
+                + f"version {self['ApplicationVersion']}. Please contact developers."
             )
         else:
             dt1 = sr.groupdict()
-            self['recording_opened'] = dateutil.parser.parse(f"{dt1['date']} {dt1['time']}")
+            self["recording_opened"] = dateutil.parser.parse(f"{dt1['date']} {dt1['time']}")
 
         # close time, if available
         sr = NlxHeader._closeDatetime1_pat.search(txt_header)
-        if not sr: sr=NlxHeader._closeDatetime2_pat.search(txt_header)
+        if not sr:
+            sr = NlxHeader._closeDatetime2_pat.search(txt_header)
         if sr:
             dt2 = sr.groupdict()
-            self['recording_closed'] = dateutil.parser.parse(f"{dt2['date']} {dt2['time']}")
+            self["recording_closed"] = dateutil.parser.parse(f"{dt2['date']} {dt2['time']}")
 
     def type_of_recording(self):
         """
diff --git a/neo/rawio/neuronexusrawio.py b/neo/rawio/neuronexusrawio.py
@@ -132,7 +132,7 @@ def _parse_header(self):
         self._n_samples, self._n_channels = self.metadata["status"]["shape"]
         # Stored as a simple float32 binary file
         BINARY_DTYPE = "float32"
-        TIMESTAMP_DTYPE = "int64" # this is from the allego sample reader timestamps are np.int64
+        TIMESTAMP_DTYPE = "int64"  # this is from the allego sample reader timestamps are np.int64
         binary_file = self.binary_file
         timestamp_file = self.timestamp_file
 
@@ -150,7 +150,7 @@ def _parse_header(self):
         # Make the memory map for timestamp
         self._timestamps = np.memmap(
             timestamp_file,
-            dtype=TIMESTAMP_DTYPE,  
+            dtype=TIMESTAMP_DTYPE,
             mode="r",
             offset=0,  # headerless binary file
         )
diff --git a/neo/rawio/spikeglxrawio.py b/neo/rawio/spikeglxrawio.py
@@ -184,8 +184,8 @@ def _parse_header(self):
                 chan_id = f"{stream_name}#{chan_name}"
 
                 # Separate sync channel in its own stream
-                is_sync_channel = "SY" in chan_name  and not self.load_sync_channel
-                if is_sync_channel :
+                is_sync_channel = "SY" in chan_name and not self.load_sync_channel
+                if is_sync_channel:
                     # This is a sync channel and should be added as its own stream
                     sync_stream_id = f"{stream_name}-SYNC"
                     sync_stream_id_to_buffer_id[sync_stream_id] = buffer_id
@@ -387,7 +387,7 @@ def scan_files(dirname):
                 continue
             meta_filename = Path(root) / file
             bin_filename = meta_filename.with_suffix(".bin")
-                
+
             if meta_filename.exists() and bin_filename.exists():
                 meta = read_meta_file(meta_filename)
                 info = extract_stream_info(meta_filename, meta)
@@ -401,6 +401,7 @@ def scan_files(dirname):
 
     return info_list
 
+
 def _add_segment_order(info_list):
     """
     Uses gate and trigger numbers to construct a segment index (`seg_index`) for each signal in `info_list`.
@@ -413,7 +414,7 @@ def _add_segment_order(info_list):
     """
     # This sets non-integers values before integers
     normalize = lambda x: x if isinstance(x, int) else -1
-    
+
     # Segment index is determined by the gate_num and trigger_num in that order
     def get_segment_tuple(info):
         # Create a key from the normalized gate_num and trigger_num
@@ -475,7 +476,7 @@ def parse_spikeglx_fname(fname):
     stream_kind: str or None
         The data type identifier, "lf", "ap", "obx", or None
     """
-    
+
     # Standard case: contains gate, trigger, device, and stream kind
     # Example: Noise4Sam_g0_t0.imec0.ap
     # Format:  {run_name}_g{gate_num}_t{trigger_num}.{device}.{stream_kind}
@@ -502,7 +503,7 @@ def parse_spikeglx_fname(fname):
         gd = match.groupdict()
         return gd["run_name"], int(gd["gate_num"]), "cat", gd["device"], gd["stream_kind"]
 
-    # OneBox case: ends in .obx 
+    # OneBox case: ends in .obx
     # Example: myRun_g0_t0.obx0.obx
     # Format:  {run_name}_g{gate_num}_t{trigger_num}.{device}.obx
     # Regex tokens:
@@ -641,7 +642,7 @@ def extract_stream_info(meta_file, meta):
         device = fname.split(".")[-2] if "." in fname else device
         stream_kind = ""
         units = "V"
-        
+
         # OneBox gain calculation
         # V = i * Vmax / Imax where Imax = obMaxInt, Vmax = obAiRangeMax
         # See: https://billkarsh.github.io/SpikeGLX/Sgl_help/Metadata_30.html
@@ -669,7 +670,7 @@ def extract_stream_info(meta_file, meta):
     probe_slot = meta.get("imDatPrb_slot", None)
     probe_port = meta.get("imDatPrb_port", None)
     probe_dock = meta.get("imDatPrb_dock", None)
-    
+
     # OneBox specific metadata
     obx_slot = meta.get("imDatObx_slot", None)
 
@@ -697,10 +698,10 @@ def extract_stream_info(meta_file, meta):
     info["probe_port"] = int(probe_port) if probe_port else None
     info["probe_dock"] = int(probe_dock) if probe_dock else None
     info["obx_slot"] = int(obx_slot) if obx_slot else None
-    
+
     # Add device index
     if info.get("device_kind") == "imec":
-        info["device_index"]  = info["device"].split("imec")[-1]
+        info["device_index"] = info["device"].split("imec")[-1]
     elif info.get("device_kind") == "obx":
         info["device_index"] = info["device"].split("obx")[-1]
     else:
@@ -732,5 +733,4 @@ def extract_stream_info(meta_file, meta):
         info["digital_channels"] = [channel for channel in info["channel_names"] if channel.startswith("XD")]
         info["analog_channels"] = [channel for channel in info["channel_names"] if channel.startswith("XA")]
 
-
     return info
diff --git a/neo/test/rawiotest/test_neuralynxrawio.py b/neo/test/rawiotest/test_neuralynxrawio.py
