More spellcheck; Markdown linting

Author: CBroz1

.markdownlint.yaml

@@ -0,0 +1,16 @@
+# Markdown Linter configuration for docs
+# https://github.com/DavidAnson/markdownlint
+# https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
+MD009: false # permit trailing spaces
+MD007: false # List indenting - permit 4 spaces
+MD013:
+    line_length: "88" # Line length limits
+    tables: false # disable for tables
+    headings: false # disable for headings
+MD030: false # Number of spaces after a list
+MD033: # HTML elements allowed
+    allowed_elements:
+        - "br"
+MD034: false # Permit bare URLs
+MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
+MD046: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling

CHANGELOG.md

@@ -6,19 +6,23 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 ## [0.2.2] - 2022-01-11
 
 + Bugfix - Revert import order in `__init__.py` to avoid circular import error.
-+ Update - `.pre-commit-config.yaml` to disable automatic positioning of import statement at the top.
++ Update - `.pre-commit-config.yaml` to disable automatic positioning of import
+  statement at the top.
 + Bugfix - Update docstrings to render API for documentation website.
 
 ## [0.2.1] - 2022-01-06
 
-+ Add - `build_electrode_layouts` function in `probe.py` to compute the electrode layout for all types of probes.
-+ Update - parameterize run_CatGT step from parameters retrieved from `ClusteringParamSet` table
++ Add - `build_electrode_layouts` function in `probe.py` to compute the electrode layout
+  for all types of probes.
++ Update - parameterize run_CatGT step from parameters retrieved from
+  `ClusteringParamSet` table
 + Update - clustering step, update duration for "median_subtraction" step
 + Bugfix - handles single probe recording in "Neuropix-PXI" format
 + Update - safeguard in creating/inserting probe types upon probe activation
 + Add - quality control metric dashboard
 + Update & fix docstrings
-+ Update - `ephys_report.UnitLevelReport` to add `ephys.ClusterQualityLabel` as a foreign key reference
++ Update - `ephys_report.UnitLevelReport` to add `ephys.ClusterQualityLabel` as a
+  foreign key reference
 + Add - `.pre-commit-config.yaml`
 
 ## [0.2.0] - 2022-10-28
@@ -28,15 +32,17 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - Add `ephys_no_curation` and routines to trigger spike-sorting analysis
   using Kilosort (2.0, 2.5)
 + Add - mkdocs for Element Documentation
-+ Add - New `QualityMetrics` table to store clusters' and waveforms' metrics after the spike sorting analysis.
++ Add - New `QualityMetrics` table to store clusters' and waveforms' metrics after the
+  spike sorting analysis.
 
 ## [0.1.4] - 2022-07-11
 
 + Bugfix - Handle case where `spike_depths` data is present.
 
 ## [0.1.3] - 2022-06-16
 
-+ Update - Allow for the `precluster_output_dir` attribute to be nullable when no pre-clustering is performed.
++ Update - Allow for the `precluster_output_dir` attribute to be nullable when no
+  pre-clustering is performed.
 
 ## [0.1.2] - 2022-06-09
 
@@ -49,7 +55,8 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 ## [0.1.0] - 2022-05-26
 
 + Update - Rename module for acute probe insertions from `ephys.py` to `ephys_acute.py`.
-+ Add - Module for pre-clustering steps (`ephys_precluster.py`), which is built off of `ephys_acute.py`.
++ Add - Module for pre-clustering steps (`ephys_precluster.py`), which is built off of
+  `ephys_acute.py`.
 + Add - Module for chronic probe insertions (`ephys_chronic.py`).
 + Bugfix - Missing `fileTimeSecs` key in SpikeGLX meta file.
 + Update - Move common functions to `element-interface` package.
@@ -59,7 +66,6 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
 
-
 ## [0.1.0b0] - 2021-05-07
 
 + Update - First beta release
@@ -72,7 +78,6 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS,
   2.0 - MS
 
-
 [0.2.2]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.2
 [0.2.1]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.1
 [0.2.0]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.0

CODE_OF_CONDUCT.md

@@ -1,4 +1,3 @@
-
 # Contributor Covenant Code of Conduct
 
 ## Our Pledge

CONTRIBUTING.md

@@ -1,3 +1,5 @@
 # Contribution Guidelines
 
-This project follows the [DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/). Please reference the link for more full details.
+This project follows the
+[DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/).
+Please reference the link for more full details.

cspell.json

@@ -16,34 +16,46 @@
         "./images/*"
     ],
     "words": [
+        "acorr",
         "aggr",
+        "Alessio",
+        "Andreas",
         "apmeta",
         "arange",
         "asarray",
         "astype",
         "autocorrelogram",
+        "Axona",
         "bbins",
         "bdist",
         "Binarize",
+        "Brody",
+        "Buccino",
         "catgt",
         "cbar",
         "cbin",
         "cdat",
         "Chans",
         "chans",
         "chns",
+        "Clust",
+        "clusterings",
         "cmap",
         "correlogram",
         "correlograms",
+        "curations",
+        "DANDI",
         "decomp",
         "DISTRO",
         "djbase",
         "dtype",
         "ecephys",
+        "electrophysiogical",
         "elif",
         "Ephys",
         "gblcar",
         "gfix",
+        "HHMI",
         "hstack",
         "ibllib",
         "ifnull",
@@ -58,44 +70,60 @@
         "inlinehilite",
         "ipywidgets",
         "kcoords",
+        "Klusta",
+        "Kwik",
         "lfmeta",
         "linenums",
         "mdict",
+        "Mesoscale",
         "mkdocs",
         "mkdocstrings",
+        "Moser",
         "mtscomp",
         "Nchan",
         "nchan",
         "ndarray",
         "ndim",
         "ndimage",
+        "Neuralynx",
         "NEURO",
+        "Neurodata",
         "Neuropix",
+        "neuropixel",
         "NeuroPixels",
         "oebin",
         "openephys",
         "openephys",
         "openpyxl",
         "phylog",
         "plotly",
+        "PSTH",
         "pykilosort",
         "pymdownx",
         "pynwb",
         "pyopenephys",
         "pyplot",
         "pytest",
+        "Reimer",
         "repolarization",
         "Roboto",
+        "RRID",
+        "Rxiv",
+        "Sasaki",
         "scipy",
         "sdist",
+        "Siegle",
         "sess",
         "SGLX",
+        "Shen",
+        "Sitonic",
         "spikeglx",
         "spkcount",
-        "Stereotaxic","acorr",
+        "Stereotaxic",
         "tcat",
         "tickvals",
         "tofile",
+        "Tolias",
         "vline",
         "Vmax",
         "vmax",
@@ -108,6 +136,7 @@
         "xlim",
         "XPOS",
         "xtick",
+        "Yatsenko",
         "yaxes",
         "yaxis",
         "ycoord",

docs/src/changelog.md

@@ -0,0 +1 @@
+../../CHANGELOG.md

docs/src/changelog.md

@@ -1,7 +1,11 @@
 # Citation
 
-If your work uses this Element, please cite the following manuscript and Research Resource Identifier (RRID):
+If your work uses this Element, please cite the following manuscript and Research
+Resource Identifier (RRID):
 
-+ Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
++ Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D,
+  Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for
+  Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
 
-+ DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) - Element Array Electrophysiology (version {{ PATCH_VERSION }})
++ DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) -
+  Element Array Electrophysiology (version {{ PATCH_VERSION }})