Add codespell - config, workflow, fixed some typos and unified/remove…

…d a few imports (#471)

Adds spell checking and fixes typos

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@master

franklab_scripts/alter_tables.py

@@ -35,7 +35,7 @@ def update_cls(cls):
             # some enum definitions will prompt alter() even when there has not been a change
             # NOTE: datajoint does not allow primary keys to be altered yet
             # this includes changing the length of a varchar primary key
-            # (other tables use this primary key, so constraints would probably have to be removed and readded)
+            # (other tables use this primary key, so constraints would probably have to be removed and re-added)
             cls.alter()
         except Exception as e:
             print("ERROR:", e)

franklab_scripts/nightly_cleanup.py

@@ -7,7 +7,6 @@
 
 import numpy as np
 
-import spyglass as nd
 from spyglass.decoding.clusterless import MarkParameters, UnitMarkParameters, UnitMarks
 
 warnings.simplefilter("ignore", category=DeprecationWarning)

franklab_scripts/sort.py

@@ -1,7 +1,7 @@
 import os
 from pathlib import Path
 
-import spyglass as nd
+import spyglass as sg
 
 
 def main():
@@ -14,10 +14,10 @@ def main():
     os.environ["SPIKE_SORTING_STORAGE_DIR"] = str(data_dir / "spikesorting")
 
     # session_id = 'jaq_01'
-    # nwb_file_name = (nd.common.Session() & {'session_id': session_id}).fetch1('nwb_file_name')
+    # nwb_file_name = (sg.common.Session() & {'session_id': session_id}).fetch1('nwb_file_name')
     nwb_file_name = "beans20190718-trim_.nwb"
 
-    nd.common.SpikeSorting().populate()
+    sg.common.SpikeSorting().populate()
 
 
 if __name__ == "__main__":

pyproject.toml

@@ -69,3 +69,8 @@ spyglass_cli = "spyglass.cli:cli"
 
 [tool.black]
 # line-length = 120
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,*.ipynb'
+# Nevers - name in Citation
+ignore-words-list = 'nevers'

src/spyglass/cli/cli.py

@@ -14,9 +14,9 @@ def cli():
 )
 @click.argument("nwb_file_name")
 def insert_session(nwb_file_name: str):
-    import spyglass as nd
+    import spyglass as sg
 
-    nd.insert_sessions(nwb_file_name)
+    sg.insert_sessions(nwb_file_name)
 
 
 @click.command(help="List all sessions")
@@ -416,7 +416,7 @@ def run_spike_sorting(yaml_file_name: Union[str, None]):
     nds.SpikeSorting.populate([(nds.SpikeSortingSelection & sorting_key).proj()])
 
 
-@click.command(help="List spike sortings for a session.")
+@click.command(help="List spike sorting for a session.")
 @click.argument("nwb_file_name")
 def list_spike_sortings(nwb_file_name: str):
     import spyglass.spikesorting as nds

src/spyglass/common/common_lab.py

@@ -106,7 +106,7 @@ def create_new_team(
             if not len(query):
                 print(
                     f"Please add the Google user ID for {team_member} in the LabMember.LabMemberInfo table "
-                    "if you want to give them permission to manually curate sortings by this team."
+                    "if you want to give them permission to manually curate sorting by this team."
                 )
             labteammember_dict = dict()
             labteammember_dict["team_name"] = team_name

src/spyglass/common/common_nwbfile.py

@@ -133,7 +133,7 @@ class AnalysisNwbfile(dj.Manual):
     -> Nwbfile                                     # name of the parent NWB file. Used for naming and metadata copy
     analysis_file_abs_path: filepath@analysis      # the full path to the file
     analysis_file_description = "": varchar(2000)  # an optional description of this analysis
-    analysis_parameters = NULL: blob               # additional relevant parmeters. Currently used only for analyses
+    analysis_parameters = NULL: blob               # additional relevant parameters. Currently used only for analyses
                                                    # that span multiple NWB files
     INDEX (analysis_file_abs_path)
     """

src/spyglass/common/common_position.py

@@ -647,7 +647,7 @@ def get_video_frame(self):
 @schema
 class PositionVideo(dj.Computed):
     """Creates a video of the computed head position and orientation as well as
-    the original LED positions overlayed on the video of the animal.
+    the original LED positions overlaid on the video of the animal.
 
     Use for debugging the effect of position extraction parameters."""
 

src/spyglass/figurl_views/SpikeSortingView.py

@@ -12,7 +12,7 @@
 @schema
 class SpikeSortingView(dj.Computed):
     definition = """
-    # Schema for storing figurl views of spike sortings
+    # Schema for storing figurl views of spike sorting
     -> SpikeSorting
     ---
     figurl: varchar(10000)

src/spyglass/spikesorting/curation_figurl.py

@@ -121,7 +121,7 @@ def _generate_the_figurl(
         max_num_snippets_per_segment=100,
         channel_neighborhood_size=7,
     )
-    # create a fake unit similiarity matrix (for future reference)
+    # create a fake unit similarity matrix (for future reference)
     # similarity_scores = []
     # for u1 in X.unit_ids:
     #     for u2 in X.unit_ids:

src/spyglass/spikesorting/sortingview_helper_fn.py

@@ -80,7 +80,7 @@ def _generate_url(
         channel_neighborhood_size=7,
     )
 
-    # create a fake unit similiarity matrix
+    # create a fake unit similarity matrix
     # similarity_scores = []
     # for u1 in X.unit_ids:
     #     for u2 in X.unit_ids:

src/spyglass/spikesorting/spikesorting_curation.py

@@ -39,7 +39,7 @@ def apply_merge_groups_to_sorting(
 class Curation(dj.Manual):
     definition = """
     # Stores each spike sorting; similar to IntervalList
-    curation_id: int # a number correponding to the index of this curation
+    curation_id: int # a number corresponding to the index of this curation
     -> SpikeSorting
     ---
     parent_curation_id=-1: int
@@ -994,7 +994,7 @@ def get_included_units(self, curated_sorting_key, unit_inclusion_param_name):
         Parameters
         ----------
         curated_sorting_key : dict
-            key to select a set of curated sortings
+            key to select a set of curated sorting
         unit_inclusion_param_name : str
             name of a unit inclusion parameter entry
 

src/spyglass/spikesorting/spikesorting_recording.py

@@ -140,7 +140,7 @@ def set_group_by_shank(
                 ]
                 if (
                     omit_unitrode and len(shank_elect) == 1
-                ):  # ommit unitrodes if indicated
+                ):  # omit unitrodes if indicated
                     print(
                         f"Omitting electrode group {e_group}, shank {shank} from sort groups because unitrode."
                     )
@@ -288,7 +288,7 @@ def get_geometry(self, sort_group_id, nwb_file_name):
                     n_found += 1
                 else:
                     Warning(
-                        "Relative electrode locations have three coordinates; only two are currenlty supported"
+                        "Relative electrode locations have three coordinates; only two are currently supported"
                     )
         return np.ndarray.tolist(geometry)
 

src/spyglass/spikesorting/spikesorting_sorting.py

@@ -288,7 +288,7 @@ def _get_sorting_name(key):
         sorting_name = recording_name + "_" + str(uuid.uuid4())[0:8] + "_spikesorting"
         return sorting_name
 
-    # TODO: write a function to import sortings done outside of dj
+    # TODO: write a function to import sorting done outside of dj
 
     def _import_sorting(self, key):
         raise NotImplementedError

src/spyglass/utils/dj_helper_fn.py

@@ -117,7 +117,7 @@ def fetch_nwb(query_expression, nwb_master, *attrs, **kwargs):
 
 
 def _get_nwb_object(objects, object_id):
-    """Retreive NWB object and try to convert to dataframe if possible"""
+    """Retrieve NWB object and try to convert to dataframe if possible"""
     try:
         return objects[object_id].to_dataframe()
     except AttributeError: