WIP: Spellcheck. Remove debug params. Remove assigned lambda E713

notebooks/14_Theta.ipynb

@@ -594,7 +594,7 @@
     "\n",
     "We can overlay theta and detected phase for each electrode.\n",
     "\n",
-    "_Note:_ The red horizontal line indicates phase 0, corresponding to the trough\n",
+    "_Note:_ The red horizontal line indicates phase 0, corresponding to the through\n",
     "of theta."
    ]
   },

notebooks/20_Position_Trodes.ipynb

@@ -142,7 +142,7 @@
     "available. To adjust the default, insert a new set into this table. The\n",
     "parameters are...\n",
     "\n",
-    "- `max_separation`, default 9 cm: maximium acceptable distance between red and\n",
+    "- `max_separation`, default 9 cm: maximum acceptable distance between red and\n",
     "  green LEDs.\n",
     "  - If exceeded, the times are marked as NaNs and inferred by interpolation.\n",
     "  - Useful when the inferred LED position tracks a reflection instead of the\n",

notebooks/24_Linearization.ipynb

@@ -87,7 +87,6 @@
     "\n",
     "import spyglass.common as sgc\n",
     "import spyglass.position.v1 as sgp\n",
-    "import spyglass as nd\n",
     "\n",
     "# ignore datajoint+jupyter async warnings\n",
     "import warnings\n",
@@ -1501,7 +1500,7 @@
     "    + 1\n",
     ")\n",
     "video_info = (\n",
-    "    nd.common.common_behav.VideoFile()\n",
+    "    sgc.common_behav.VideoFile()\n",
     "    & {\"nwb_file_name\": key[\"nwb_file_name\"], \"epoch\": epoch}\n",
     ").fetch1()\n",
     "\n",

notebooks/33_Decoding_Clusterless.ipynb

@@ -32,8 +32,8 @@
     "  [extracted marks](./31_Extract_Mark_Indicators.ipynb), as well as loaded \n",
     "  position data. If 1D decoding, this data should also be\n",
     "  [linearized](./24_Linearization.ipynb).\n",
-    "- Ths tutorial also assumes you're familiar with how to run processes on GPU, as\n",
-    "  presented in [this notebook](./32_Decoding_with_GPUs.ipynb)\n",
+    "- This tutorial also assumes you're familiar with how to run processes on GPU, \n",
+    "  as presented in [this notebook](./32_Decoding_with_GPUs.ipynb)\n",
     "\n",
     "Clusterless decoding can be performed on either 1D or 2D data. A few steps in\n",
     "this notebook will refer to a `decode_1d` variable set in \n",
@@ -143,10 +143,10 @@
    "source": [
     "First, we'll fetch marks with `fetch_xarray`, which provides a labeled array of\n",
     "shape (n_time, n_mark_features, n_electrodes). Time is in 2 ms bins with either\n",
-    "`NaN` if no spike occured or the value of the spike features.\n",
+    "`NaN` if no spike occurred or the value of the spike features.\n",
     "\n",
     "If there is >1 spike per time bin per tetrode, we take an an average of the\n",
-    "marks. Ideally, we would use all the marks, this is a rare occurance and\n",
+    "marks. Ideally, we would use all the marks, this is a rare occurrence and\n",
     "decoding is generally robust to the averaging."
    ]
   },

notebooks/py_scripts/14_Theta.py

@@ -128,7 +128,7 @@
 #
 # We can overlay theta and detected phase for each electrode.
 #
-# _Note:_ The red horizontal line indicates phase 0, corresponding to the trough
+# _Note:_ The red horizontal line indicates phase 0, corresponding to the through
 # of theta.
 
 # +

notebooks/py_scripts/20_Position_Trodes.py

@@ -87,7 +87,7 @@
 # available. To adjust the default, insert a new set into this table. The
 # parameters are...
 #
-# - `max_separation`, default 9 cm: maximium acceptable distance between red and
+# - `max_separation`, default 9 cm: maximum acceptable distance between red and
 #   green LEDs.
 #   - If exceeded, the times are marked as NaNs and inferred by interpolation.
 #   - Useful when the inferred LED position tracks a reflection instead of the

notebooks/py_scripts/24_Linearization.py

@@ -54,7 +54,6 @@
 
 import spyglass.common as sgc
 import spyglass.position.v1 as sgp
-import spyglass as nd
 
 # ignore datajoint+jupyter async warnings
 import warnings
@@ -335,7 +334,7 @@
     + 1
 )
 video_info = (
-    nd.common.common_behav.VideoFile()
+    sgc.common_behav.VideoFile()
     & {"nwb_file_name": key["nwb_file_name"], "epoch": epoch}
 ).fetch1()
 

notebooks/py_scripts/33_Decoding_Clusterless.py

@@ -28,8 +28,8 @@
 #   [extracted marks](./31_Extract_Mark_Indicators.ipynb), as well as loaded
 #   position data. If 1D decoding, this data should also be
 #   [linearized](./24_Linearization.ipynb).
-# - Ths tutorial also assumes you're familiar with how to run processes on GPU, as
-#   presented in [this notebook](./32_Decoding_with_GPUs.ipynb)
+# - This tutorial also assumes you're familiar with how to run processes on GPU,
+#   as presented in [this notebook](./32_Decoding_with_GPUs.ipynb)
 #
 # Clusterless decoding can be performed on either 1D or 2D data. A few steps in
 # this notebook will refer to a `decode_1d` variable set in
@@ -87,10 +87,10 @@
 
 # First, we'll fetch marks with `fetch_xarray`, which provides a labeled array of
 # shape (n_time, n_mark_features, n_electrodes). Time is in 2 ms bins with either
-# `NaN` if no spike occured or the value of the spike features.
+# `NaN` if no spike occurred or the value of the spike features.
 #
 # If there is >1 spike per time bin per tetrode, we take an an average of the
-# marks. Ideally, we would use all the marks, this is a rare occurance and
+# marks. Ideally, we would use all the marks, this is a rare occurrence and
 # decoding is generally robust to the averaging.
 
 # +

src/spyglass/common/common_behav.py

@@ -31,7 +31,7 @@ class PositionSource(dj.Manual):
     -> IntervalList
     ---
     source: varchar(200)             # source of data (e.g., trodes, dlc)
-    import_file_name: varchar(2000)  # path to import file if importing 
+    import_file_name: varchar(2000)  # path to import file if importing
     """
 
     class SpatialSeries(dj.Part):
@@ -44,16 +44,19 @@ class SpatialSeries(dj.Part):
 
     @classmethod
     def insert_from_nwbfile(cls, nwb_file_name):
-        """Given an NWB file name, get the spatial series and interval lists from the file, add the interval
-        lists to the IntervalList table, and populate the RawPosition table if possible.
+        """Add intervals to ItervalList and PositionSource.
+
+        Given an NWB file name, get the spatial series and interval lists from
+        the file, add the interval lists to the IntervalList table, and
+        populate the RawPosition table if possible.
 
         Parameters
         ----------
         nwb_file_name : str
             The name of the NWB file.
         """
         nwbf = get_nwb_file(nwb_file_name)
-        all_pos = get_all_spatial_series(nwbf, verbose=True, old_format=False)
+        all_pos = get_all_spatial_series(nwbf, verbose=True)
         sess_key = dict(nwb_file_name=nwb_file_name)
         src_key = dict(**sess_key, source="trodes", import_file_name="")
 
@@ -81,7 +84,7 @@ def insert_from_nwbfile(cls, nwb_file_name):
                     dict(
                         **sess_key,
                         **ind_key,
-                        id=ndex,
+                        id=index,
                         name=pdict.get("name"),
                     )
                 )
@@ -189,9 +192,9 @@ def make(self, key):
         indices = (PositionSource.SpatialSeries & key).fetch("id")
 
         # incl_times = False -> don't do extra processing for valid_times
-        spat_objs = get_all_spatial_series(
-            nwbf, old_format=False, incl_times=False
-        )[PositionSource.get_epoch_num(interval_list_name)]
+        spat_objs = get_all_spatial_series(nwbf, incl_times=False)[
+            PositionSource.get_epoch_num(interval_list_name)
+        ]
 
         self.insert1(key)
         self.Object.insert(
@@ -227,7 +230,7 @@ class StateScriptFile(dj.Imported):
     """
 
     def make(self, key):
-        """Add a new row to the StateScriptFile table. Requires keys "nwb_file_name", "file_object_id"."""
+        """Add a new row to the StateScriptFile table."""
         nwb_file_name = key["nwb_file_name"]
         nwb_file_abspath = Nwbfile.get_abs_path(nwb_file_name)
         nwbf = get_nwb_file(nwb_file_abspath)
@@ -237,8 +240,8 @@ def make(self, key):
         ) or nwbf.processing.get("associated files")
         if associated_files is None:
             print(
-                f'Unable to import StateScriptFile: no processing module named "associated_files" '
-                f"found in {nwb_file_name}."
+                "Unable to import StateScriptFile: no processing module named "
+                + '"associated_files" found in {nwb_file_name}.'
             )
             return
 
@@ -247,13 +250,16 @@ def make(self, key):
                 associated_file_obj, ndx_franklab_novela.AssociatedFiles
             ):
                 print(
-                    f'Data interface {associated_file_obj.name} within "associated_files" processing module is not '
-                    f"of expected type ndx_franklab_novela.AssociatedFiles\n"
+                    f"Data interface {associated_file_obj.name} within "
+                    + '"associated_files" processing module is not '
+                    + "of expected type ndx_franklab_novela.AssociatedFiles\n"
                 )
                 return
+
             # parse the task_epochs string
-            # TODO update associated_file_obj.task_epochs to be an array of 1-based ints,
-            # not a comma-separated string of ints
+            # TODO: update associated_file_obj.task_epochs to be an array of
+            # 1-based ints, not a comma-separated string of ints
+
             epoch_list = associated_file_obj.task_epochs.split(",")
             # only insert if this is the statescript file
             print(associated_file_obj.description)
@@ -281,8 +287,9 @@ class VideoFile(dj.Imported):
 
     Notes
     -----
-    The video timestamps come from: videoTimeStamps.cameraHWSync if PTP is used.
-    If PTP is not used, the video timestamps come from videoTimeStamps.cameraHWFrameCount .
+    The video timestamps come from: videoTimeStamps.cameraHWSync if PTP is
+    used. If PTP is not used, the video timestamps come from
+    videoTimeStamps.cameraHWFrameCount .
 
     """
 
@@ -330,7 +337,9 @@ def _no_transaction_make(self, key, verbose=True):
             if isinstance(video, pynwb.image.ImageSeries):
                 video = [video]
             for video_obj in video:
-                # check to see if the times for this video_object are largely overlapping with the task epoch times
+                # check to see if the times for this video_object are largely
+                # overlapping with the task epoch times
+
                 if len(
                     interval_list_contains(valid_times, video_obj.timestamps)
                     > 0.9 * len(video_obj.timestamps)
@@ -341,7 +350,8 @@ def _no_transaction_make(self, key, verbose=True):
                         key["camera_name"] = video_obj.device.camera_name
                     else:
                         raise KeyError(
-                            f"No camera with camera_name: {camera_name} found in CameraDevice table."
+                            f"No camera with camera_name: {camera_name} found "
+                            + "in CameraDevice table."
                         )
                     key["video_file_object_id"] = video_obj.object_id
                     self.insert1(key)
@@ -365,16 +375,17 @@ def update_entries(cls, restrict={}):
             video_nwb = (cls & row).fetch_nwb()[0]
             if len(video_nwb) != 1:
                 raise ValueError(
-                    f"expecting 1 video file per entry, but {len(video_nwb)} files found"
+                    f"Expecting 1 video file per entry. {len(video_nwb)} found"
                 )
             row["camera_name"] = video_nwb[0]["video_file"].device.camera_name
             cls.update1(row=row)
 
     @classmethod
     def get_abs_path(cls, key: Dict):
-        """Return the absolute path for a stored video file given a key with the nwb_file_name and epoch number
+        """Return the absolute path for a stored video file given a key.
 
-        The SPYGLASS_VIDEO_DIR environment variable must be set.
+        Key must include the nwb_file_name and epoch number. The
+        SPYGLASS_VIDEO_DIR environment variable must be set.
 
         Parameters
         ----------

src/spyglass/position/v1/dlc_utils.py

@@ -533,15 +533,18 @@ def get_gpu_memory():
         if subproccess command errors.
     """
 
-    output_to_list = lambda x: x.decode("ascii").split("\n")[:-1]
+    def output_to_list(x):
+        return x.decode("ascii").split("\n")[:-1]
+
     query_cmd = "nvidia-smi --query-gpu=memory.used --format=csv"
     try:
         memory_use_info = output_to_list(
             subprocess.check_output(query_cmd.split(), stderr=subprocess.STDOUT)
         )[1:]
     except subprocess.CalledProcessError as err:
         raise RuntimeError(
-            f"command {err.cmd} return with error (code {err.returncode}): {err.output}"
+            f"command {err.cmd} return with error (code {err.returncode}): "
+            + f"{err.output}"
         ) from err
     memory_use_values = {
         i: int(x.split()[0]) for i, x in enumerate(memory_use_info)

src/spyglass/utils/dj_merge_tables.py

@@ -445,10 +445,19 @@ def merge_delete_parent(
         if dry_run:
             return part_parents
 
-        with cls._safe_context():
-            super().delete(cls(), **kwargs)
-            for part_parent in part_parents:
-                super().delete(part_parent, **kwargs)
+        merge_ids = cls.merge_restrict(restriction).fetch(
+            RESERVED_PRIMARY_KEY, as_dict=True
+        )
+
+        # CB: Removed transaction protection here bc 'no' confirmation resp
+        # still resulted in deletes. If re-add, consider transaction=False
+        super().delete((cls & merge_ids), **kwargs)
+
+        if cls & merge_ids:  # If 'no' on del prompt from above, skip below
+            return  # User can still abort del below, but yes/no is unlikly
+
+        for part_parent in part_parents:
+            super().delete(part_parent, **kwargs)  # add safemode=False?
 
     @classmethod
     def fetch_nwb(