Markdown lint

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

@@ -65,10 +65,10 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 ## 0.1.0a3 - 2022-01-18
 
 + Update - Notebooks
-+ Update - Move instructions to [datajoint-elements/install.md](
-     https://github.com/datajoint/datajoint-elements/blob/main/install.md).
++ Update - Move instructions to
+  [datajoint-elements/install.md](https://github.com/datajoint/datajoint-elements/blob/main/install.md).
 + Update - Docker and Compose files for new base image and added options to install
-specific forks for tests.
+  specific forks for tests.
 
 ## 0.1.0a2 - 2021-04-12
 

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://docs.datajoint.io/python/community/02-Contribute.html). 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.

README.md

@@ -1,8 +1,11 @@
 # DataJoint Workflow - Array Electrophysiology
 
 Workflow for extracellular array electrophysiology data acquired with a polytrode probe
-(e.g. [Neuropixels](https://www.neuropixels.org), Neuralynx) using the [SpikeGLX](https://github.com/billkarsh/SpikeGLX) or
-[OpenEphys](https://open-ephys.org/gui) acquisition software and processed with [MATLAB-based Kilosort](https://github.com/MouseLand/Kilosort) or [python-based Kilosort](https://github.com/MouseLand/pykilosort) spike sorting software.
+(e.g. [Neuropixels](https://www.neuropixels.org), Neuralynx) using the
+[SpikeGLX](https://github.com/billkarsh/SpikeGLX) or
+[OpenEphys](https://open-ephys.org/gui) acquisition software and processed with
+[MATLAB-based Kilosort](https://github.com/MouseLand/Kilosort) or [python-based
+Kilosort](https://github.com/MouseLand/pykilosort) spike sorting software.
 
 A complete electrophysiology workflow can be built using the DataJoint Elements.
 
@@ -14,16 +17,23 @@ A complete electrophysiology workflow can be built using the DataJoint Elements.
 This repository provides demonstrations for:
 
 1. Set up a workflow using DataJoint Elements (see
-[workflow_array_ephys/pipeline.py](workflow_array_ephys/pipeline.py))
+   [workflow_array_ephys/pipeline.py](workflow_array_ephys/pipeline.py))
+
 2. Ingestion of data/metadata based on a predefined file structure, file naming
-convention, and directory lookup methods (see
-[workflow_array_ephys/paths.py](workflow_array_ephys/paths.py)).
+   convention, and directory lookup methods (see
+   [workflow_array_ephys/paths.py](workflow_array_ephys/paths.py)).
+
 3. Ingestion of clustering results.
-4. Export of `no_curation` schema to NWB and DANDI (see [notebooks/09-NWB-export.ipynb](notebooks/09-NWB-export.ipynb)).
 
-See the [Element Array Electrophysiology documentation](https://elements.datajoint.org/description/array_ephys/) for the background information and development timeline.
+4. Export of `no_curation` schema to NWB and DANDI (see
+   [notebooks/09-NWB-export.ipynb](notebooks/09-NWB-export.ipynb)).
 
-For more information on the DataJoint Elements project, please visit <https://elements.datajoint.org>.  This work is supported by the National Institutes of Health.
+See the [Element Array Electrophysiology documentation](https://elements.datajoint.org/description/array_ephys/)
+for the background information and development timeline.
+
+For more information on the DataJoint Elements project, please visit
+<https://elements.datajoint.org>. This work is supported by the National Institutes of
+Health.
 
 ## Workflow architecture
 
@@ -38,18 +48,20 @@ schema options, selected via the DataJoint config file, with
 
 + `acute` probe insertion, with curated clustering
 + `chronic` probe insertion, with curated clustering
-+ `no-curation`, acute probe insertion with kilosort triggered clustering and supported NWB export
-+ `precluster`, acute probe insertion with pre-processing steps prior to clustering and curated clustering
++ `no-curation`, acute probe insertion with kilosort triggered clustering and supported
+  NWB export
++ `precluster`, acute probe insertion with pre-processing steps prior to clustering and
+  curated clustering
 
-![](https://raw.githubusercontent.com/datajoint/workflow-array-ephys/main/images/attached_array_ephys_element.svg)
+![Ephys Diagram](https://raw.githubusercontent.com/datajoint/workflow-array-ephys/main/images/attached_array_ephys_element.svg)
 
 Optionally, this can be used in conjunction with
 [element-event](https://github.com/datajoint/element-event)
 and [element-electrode-localization](https://github.com/datajoint/element-electrode-localization/).
 
-![](https://raw.githubusercontent.com/datajoint/workflow-array-ephys/main/images/attached_trial_analysis.svg)
+![Diagram with trial schema](https://raw.githubusercontent.com/datajoint/workflow-array-ephys/main/images/attached_trial_analysis.svg)
 
-![](https://raw.githubusercontent.com/datajoint/workflow-array-ephys/main/images/attached_electrode_localization.svg)
+![Diagram with localization schema](https://raw.githubusercontent.com/datajoint/workflow-array-ephys/main/images/attached_electrode_localization.svg)
 
 ## Installation instructions
 
@@ -63,28 +75,39 @@ Please refer to the workflow-specific
 for an in-depth explanation of how to ...
 
 1. Run the workflow ([03-process.ipynb](notebooks/03-process.ipynb)).
+
 2. Explore the data ([05-explore.ipynb](notebooks/05-explore.ipynb)).
+
 3. Examine trialized analyses, and establish downstream analyses
-([07-downstream-analysis.ipynb](notebooks/07-downstream-analysis.ipynb))
+   ([07-downstream-analysis.ipynb](notebooks/07-downstream-analysis.ipynb))
+
 4. Locate probes within the
-[Common Coordinate Framework](https://www.sciencedirect.com/science/article/pii/S0092867420304025)
-([08-electrode-localization.ipynb](notebooks/08-electrode-localization.ipynb))
+   [Common Coordinate Framework](https://www.sciencedirect.com/science/article/pii/S0092867420304025)
+   ([08-electrode-localization.ipynb](notebooks/08-electrode-localization.ipynb))
+
 5. Export to NWB and DANDI ([09-NWB-export.ipynb](notebooks/09-NWB-export.ipynb))
 
 See our YouTube tutorial for a walkthrough of the schemas and functions:
   [![YouTube tutorial](https://img.youtube.com/vi/KQlGYOBq7ow/0.jpg)](https://www.youtube.com/watch?v=KQlGYOBq7ow)
 
 ## Citation
 
-If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.
-
+If your work uses DataJoint and DataJoint Elements, please cite the respective Research
+Resource Identifiers (RRIDs) and manuscripts.
 
-* DataJoint for Python or MATLAB
-  + Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: <https://doi.org/10.1101/031658>
++ DataJoint for Python or MATLAB
+  + Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton
+    RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or
+    Python. bioRxiv. 2015 Jan 1:031658. doi: <https://doi.org/10.1101/031658>
 
-  + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for `<Select Python or MATLAB>` (version `<Enter version number>`)
+  + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint
+    for `<Select Python or MATLAB>` (version `<Enter version number>`)
 
 + DataJoint Elements
-  + 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 `<Enter version number>`)
+  + DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) -
+    Element Array Electrophysiology (version `<Enter version number>`)