Merge branch 'main' into datajoint-spikeinterface

Author: ttngu207

element_array_ephys/ephys_acute.py

@@ -185,7 +185,7 @@ def auto_generate_entries(cls, session_key):
 
                 probe_dir = meta_filepath.parent
                 try:
-                    probe_number = re.search("(imec)?\d{1}$", probe_dir.name).group()
+                    probe_number = re.search(r"(imec)?\d{1}$", probe_dir.name).group()
                     probe_number = int(probe_number.replace("imec", ""))
                 except AttributeError:
                     probe_number = meta_fp_idx

element_array_ephys/ephys_no_curation.py

@@ -190,7 +190,7 @@ def auto_generate_entries(cls, session_key):
 
                 probe_dir = meta_filepath.parent
                 try:
-                    probe_number = re.search("(imec)?\d{1}$", probe_dir.name).group()
+                    probe_number = re.search(r"(imec)?\d{1}$", probe_dir.name).group()
                     probe_number = int(probe_number.replace("imec", ""))
                 except AttributeError:
                     probe_number = meta_fp_idx

element_array_ephys/readers/kilosort.py

@@ -204,14 +204,14 @@ def extract_clustering_info(cluster_output_dir):
         is_curated = bool(np.any(curation_row))
         if creation_time is None and is_curated:
             row_meta = phylog.meta[np.where(curation_row)[0].max()]
-            datetime_str = re.search("\d{2}-\d{2}-\d{2}\s\d{2}:\d{2}:\d{2}", row_meta)
+            datetime_str = re.search(r"\d{2}-\d{2}-\d{2}\s\d{2}:\d{2}:\d{2}", row_meta)
             if datetime_str:
                 creation_time = datetime.strptime(
                     datetime_str.group(), "%Y-%m-%d %H:%M:%S"
                 )
             else:
                 creation_time = datetime.fromtimestamp(phylog_filepath.stat().st_ctime)
-                time_str = re.search("\d{2}:\d{2}:\d{2}", row_meta)
+                time_str = re.search(r"\d{2}:\d{2}:\d{2}", row_meta)
                 if time_str:
                     creation_time = datetime.combine(
                         creation_time.date(),

element_array_ephys/readers/kilosort_triggering.py

@@ -98,7 +98,7 @@ def __init__(
 
     def parse_input_filename(self):
         meta_filename = next(self._npx_input_dir.glob("*.ap.meta")).name
-        match = re.search("(.*)_g(\d)_t(\d+|cat)\.imec(\d?)\.ap\.meta", meta_filename)
+        match = re.search(r"(.*)_g(\d)_t(\d+|cat)\.imec(\d?)\.ap\.meta", meta_filename)
         session_str, gate_str, trigger_str, probe_str = match.groups()
         return session_str, gate_str, trigger_str, probe_str or "0"
 
@@ -719,7 +719,7 @@ def _get_median_subtraction_duration_from_log(self):
                         ) and previous_line.startswith("Total processing time:"):
                             # regex to search for the processing duration - a float value
                             duration = int(
-                                re.search("\d+\.?\d+", previous_line).group()
+                                re.search(r"\d+\.?\d+", previous_line).group()
                             )
                             return duration
                         previous_line = line

element_array_ephys/readers/spikeglx.py

@@ -266,7 +266,7 @@ def __init__(self, meta_filepath):
         self.probe_PN = self.meta.get("imDatPrb_pn", "3A")
 
         # Infer npx probe model (e.g. 1.0 (3A, 3B) or 2.0)
-        probe_model = self.meta.get("imDatPrb_type", 1)
+        probe_model = self.meta.get("imDatPrb_type", 0)
         if probe_model < 1:
             if "typeEnabled" in self.meta and self.probe_PN == "3A":
                 self.probe_model = "neuropixels 1.0 - 3A"

setup.py

@@ -36,7 +36,7 @@
         "plotly",
         "seaborn",
         "spikeinterface @ git+https://github.com/SpikeInterface/spikeinterface.git",
-        "scikit-image",
+        "scikit-image>=0.20",
         "nbformat>=4.2.0",
         "pyopenephys>=1.1.6",
         "element-interface @ git+https://github.com/datajoint/element-interface.git",