Spellcheck pass

CBroz1 · CBroz1 · commit ea980e9d35a7 · 2023-01-12T15:35:13.000-06:00
diff --git a/cspell.json b/cspell.json
@@ -0,0 +1,121 @@
+// cSpell Settings
+//https://github.com/streetsidesoftware/vscode-spell-checker
+{
+    "version": "0.2", // Version of the setting file.  Always 0.2
+    "language": "en", // language - current active spelling language
+    "enabledLanguageIds": [
+        "markdown", "yaml", "python"
+    ],
+    // flagWords - list of words to be always considered incorrect
+    // This is useful for offensive words and common spelling errors.
+    // For example "hte" should be "the"
+    "flagWords": [],
+    "allowCompoundWords": true,
+    "ignorePaths": [
+        "./element_array_ephys.egg-info/*",
+        "./images/*"
+    ],
+    "words": [
+        "aggr",
+        "apmeta",
+        "arange",
+        "asarray",
+        "astype",
+        "autocorrelogram",
+        "bbins",
+        "bdist",
+        "Binarize",
+        "catgt",
+        "cbar",
+        "cbin",
+        "cdat",
+        "Chans",
+        "chans",
+        "chns",
+        "cmap",
+        "correlogram",
+        "correlograms",
+        "decomp",
+        "DISTRO",
+        "djbase",
+        "dtype",
+        "ecephys",
+        "elif",
+        "Ephys",
+        "gblcar",
+        "gfix",
+        "hstack",
+        "ibllib",
+        "ifnull",
+        "Imax",
+        "IMAX",
+        "imax",
+        "imec",
+        "imread",
+        "imro",
+        "imrotbl",
+        "imshow",
+        "inlinehilite",
+        "ipywidgets",
+        "kcoords",
+        "lfmeta",
+        "linenums",
+        "mdict",
+        "mkdocs",
+        "mkdocstrings",
+        "mtscomp",
+        "Nchan",
+        "nchan",
+        "ndarray",
+        "ndim",
+        "ndimage",
+        "NEURO",
+        "Neuropix",
+        "NeuroPixels",
+        "oebin",
+        "openephys",
+        "openephys",
+        "openpyxl",
+        "phylog",
+        "plotly",
+        "pykilosort",
+        "pymdownx",
+        "pynwb",
+        "pyopenephys",
+        "pyplot",
+        "pytest",
+        "repolarization",
+        "Roboto",
+        "scipy",
+        "sdist",
+        "sess",
+        "SGLX",
+        "spikeglx",
+        "spkcount",
+        "Stereotaxic","acorr",
+        "tcat",
+        "tickvals",
+        "tofile",
+        "vline",
+        "Vmax",
+        "vmax",
+        "xanchor",
+        "xaxes",
+        "xaxis",
+        "xcoords",
+        "xcorr",
+        "xlabel",
+        "xlim",
+        "XPOS",
+        "xtick",
+        "yaxes",
+        "yaxis",
+        "ycoord",
+        "ycoords",
+        "ylabel",
+        "ylim",
+        "YPOS",
+        "yref",
+        "yticks"
+    ]
+}
diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml
@@ -43,7 +43,7 @@ nav:
 #     HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
 #     ```
 # 02. Site analytics depend on a local environment variable GOOGLE_ANALYTICS_KEY
-#     You can find this in LastPass or declare with any string to suprress errors
+#     You can find this in LastPass or declare with any string to suppress errors
 # 03. The API section will pull docstrings.
 #     A. Follow google styleguide e.g., 
 #        https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
diff --git a/element_array_ephys/ephys_acute.py b/element_array_ephys/ephys_acute.py
@@ -32,7 +32,7 @@ def activate(
 
     Args:
         ephys_schema_name (str): A string containing the name of the ephys schema.
-        probe_schema_name (str): A string containing the name of the probe scehma.
+        probe_schema_name (str): A string containing the name of the probe schema.
         create_schema (bool): If True, schema will be created in the database.
         create_tables (bool): If True, tables related to the schema will be created in the database.
         linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
diff --git a/element_array_ephys/ephys_chronic.py b/element_array_ephys/ephys_chronic.py
@@ -31,7 +31,7 @@ def activate(
 
     Args:
         ephys_schema_name (str): A string containing the name of the ephys schema.
-        probe_schema_name (str): A string containing the name of the probe scehma.
+        probe_schema_name (str): A string containing the name of the probe schema.
         create_schema (bool): If True, schema will be created in the database.
         create_tables (bool): If True, tables related to the schema will be created in the database.
         linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
diff --git a/element_array_ephys/ephys_no_curation.py b/element_array_ephys/ephys_no_curation.py
@@ -32,7 +32,7 @@ def activate(
 
     Args:
         ephys_schema_name (str): A string containing the name of the ephys schema.
-        probe_schema_name (str): A string containing the name of the probe scehma.
+        probe_schema_name (str): A string containing the name of the probe schema.
         create_schema (bool): If True, schema will be created in the database.
         create_tables (bool): If True, tables related to the schema will be created in the database.
         linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
diff --git a/element_array_ephys/ephys_precluster.py b/element_array_ephys/ephys_precluster.py
@@ -27,7 +27,7 @@ def activate(
 
     Args:
         ephys_schema_name (str): A string containing the name of the ephys schema.
-        probe_schema_name (str): A string containing the name of the probe scehma.
+        probe_schema_name (str): A string containing the name of the probe schema.
         create_schema (bool): If True, schema will be created in the database.
         create_tables (bool): If True, tables related to the schema will be created in the database.
         linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
@@ -436,7 +436,7 @@ class Step(dj.Part):
 
 @schema
 class PreClusterTask(dj.Manual):
-    """Defines a pre-clusting task ready to be run.
+    """Defines a pre-clustering task ready to be run.
 
     Attributes:
         EphysRecording (foreign key): EphysRecording primary key.
diff --git a/element_array_ephys/plotting/qc.py b/element_array_ephys/plotting/qc.py
@@ -28,7 +28,7 @@ def __init__(
             key (dict, optional): key from ephys.QualityMetric table. Defaults to None.
             scale (float, optional): Scale at which to render figure. Defaults to 1.4.
             fig_width (int, optional): Figure width in pixels. Defaults to 800.
-            amplitude_cutoff_maximum (float, optional): Cutoff for unit ampliude in
+            amplitude_cutoff_maximum (float, optional): Cutoff for unit amplitude in
                 visualizations. Defaults to None.
             presence_ratio_minimum (float, optional): Cutoff for presence ratio in
                 visualizations. Defaults to None.
@@ -61,7 +61,7 @@ def key(self) -> dict:
     def key(self, key: dict):
         """Use class_instance.key = your_key to reset key"""
         if key not in self._ephys.QualityMetrics.fetch("KEY"):
-            # If not already full key, check if unquely identifies entry
+            # If not already full key, check if uniquely identifies entry
             key = (self._ephys.QualityMetrics & key).fetch1("KEY")
         self._key = key
 
@@ -127,7 +127,7 @@ def units(self) -> pd.DataFrame:
     def _format_fig(
         self, fig: go.Figure = None, scale: float = None, ratio: float = 1.0
     ) -> go.Figure:
-        """Return formatted figure or apply prmatting to existing figure
+        """Return formatted figure or apply formatting to existing figure
 
         Args:
             fig (go.Figure, optional): Apply formatting to this plotly graph object
@@ -252,7 +252,7 @@ def get_grid(self, n_columns: int = 4, scale: float = 1.0) -> go.Figure:
         """Plot grid of histograms as subplots in go.Figure using n_columns
 
         Args:
-            n_columns (int, optional): Number of colums in grid. Defaults to 4.
+            n_columns (int, optional): Number of column in grid. Defaults to 4.
             scale (float, optional): Scale to render fig. Defaults to scale at class
                 init, 1.
 
@@ -334,7 +334,7 @@ def get_grid(self, n_columns: int = 4, scale: float = 1.0) -> go.Figure:
 
     @property
     def plot_list(self):
-        """List of plots that can be rendered inidividually by name or as grid"""
+        """List of plots that can be rendered individually by name or as grid"""
         if not self._plots:
             _ = self.plots
         return [plot for plot in self._plots]
