Merge branch 'datajoint:main' into main

Author: JaerongA

CHANGELOG.md

@@ -38,8 +38,8 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - NWB export function
 
 ## [0.1.0b4] - 2021-11-29
-### Added
-+ Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
+
++ Add - Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
 
 
 ## [0.1.0b0] - 2021-05-07

README.md

@@ -1,9 +1,12 @@
 # DataJoint Element - Array Electrophysiology Element
 
-DataJoint Element for extracellular array electrophysiology. 
-DataJoint Elements collectively standardize and automate data collection and analysis for neuroscience experiments.  Each Element is a modular pipeline for data storage and processing with corresponding database tables that can be combined with other Elements to assemble a fully functional pipeline.
+DataJoint Element for extracellular array electrophysiology. DataJoint Elements
+collectively standardize and automate data collection and analysis for neuroscience
+experiments.  Each Element is a modular pipeline for data storage and processing with
+corresponding database tables that can be combined with other Elements to assemble a
+fully functional pipeline.
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
 
 Installation and usage instructions can be found at the 
 [Element documentation](datajoint.com/docs/elements/element-array-ephys).
-
-![element-array-ephys diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)

docs/mkdocs.yaml

@@ -68,8 +68,8 @@ theme:
   name: material
   custom_dir: src/.overrides
   icon:
-    logo: main/project-logo-black
-  favicon: assets/images/project-logo-color.png
+    logo: main/company-logo
+  favicon: assets/images/company-logo-blue.png
   features:
     - toc.integrate
     - content.code.annotate
@@ -127,44 +127,38 @@ extra:
   analytics:
     provider: google
     property: !ENV GOOGLE_ANALYTICS_KEY
-    feedback:
-      title: Was this page helpful?
-      ratings:
-        - icon: material/emoticon-happy-outline
-          name: This page was helpful
-          data: 1
-          note: >-
-            Thanks for your feedback!
-        - icon: material/emoticon-sad-outline
-          name: This page could be improved
-          data: 0
-          note: >-
-            Thanks for your feedback!
   version:
     provider: mike
   social:
     - icon: main/company-logo
-      link: https://www.datajoint.com/
-    - icon: fontawesome/solid/ticket
-      link: https://support.djneuro.io/portal/en/home
+      link: https://www.datajoint.com
+      name: DataJoint
     - icon: fontawesome/brands/slack
       link: https://datajoint.slack.com
+      name: Slack
     - icon: fontawesome/brands/linkedin
       link: https://www.linkedin.com/company/datajoint
+      name: LinkedIn
     - icon: fontawesome/brands/twitter
-      link: https://twitter.com/DataJointIO
+      link: https://twitter.com/datajoint
+      name: Twitter
     - icon: fontawesome/brands/github
       link: https://github.com/datajoint
+      name: GitHub
     - icon: fontawesome/brands/docker
       link: https://hub.docker.com/u/datajoint
+      name: DockerHub
     - icon: fontawesome/brands/python
       link: https://pypi.org/user/datajointbot
+      name: PyPI
     - icon: fontawesome/brands/stack-overflow
       link: https://stackoverflow.com/questions/tagged/datajoint
+      name: StackOverflow
     - icon: fontawesome/brands/youtube
       link: https://www.youtube.com/channel/UCdeCuFOTCXlVMRzh6Wk-lGg
+      name: YouTube
 extra_css:
   - assets/stylesheets/extra.css
 
 extra_javascript:
-  - https://js-na1.hs-scripts.com/23133402.js  # HubSpot chatbot
+  - https://js-na1.hs-scripts.com/23133402.js  # HubSpot chatbot

docs/src/.overrides/.icons/main/company-logo.svg

@@ -6,6 +6,40 @@
     --dj-white: #ffffff;
 }
 
+/* footer previous/next navigation */
+.md-footer__inner:not([hidden]) {
+    display: none
+}
+
+/* footer social icons */
+html a[title="DataJoint"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="Slack"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="LinkedIn"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="Twitter"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="GitHub"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="DockerHub"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="PyPI"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="StackOverflow"].md-social__link svg {
+    color: var(--dj-primary);
+}
+html a[title="YouTube"].md-social__link svg {
+    color: var(--dj-primary);
+}
+
 [data-md-color-scheme="datajoint"] {
     /* ribbon */
     /* ribbon + markdown heading expansion */
@@ -29,7 +63,7 @@
 
     /* footer */
     /* previous/next text */
-    --md-footer-fg-color: var(--dj-primary);
+    /* --md-footer-fg-color: var(--dj-primary); */
 }
 
 [data-md-color-scheme="slate"] {
@@ -55,5 +89,5 @@
 
     /* footer */
     /* previous/next text */
-    --md-footer-fg-color: var(--dj-white);
-}
+    /* --md-footer-fg-color: var(--dj-white); */
+}

docs/src/.overrides/.icons/main/project-logo-black.svg

@@ -55,7 +55,17 @@ Over the past few years, several labs have developed DataJoint-based data manage
 
 Each of the DataJoint Elements creates a set of tables for common neuroscience data modalities to organize, preprocess, and analyze data. Each node in the following diagram is a table within the Element or a table connected to the Element.
 
-![element-array-ephys diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
+### `ephys_acute` module
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
+
+### `ephys_chronic` module
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_chronic.svg)
+
+### `ephys_precluster` module
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_precluster.svg)
 
 ### `subject` schema ([API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/subject))
 - Although not required, most choose to connect the `Session` table to a `Subject` table.

docs/src/.overrides/assets/images/company-logo-blue.png

@@ -1,20 +1,29 @@
 # Element Array Electrophysiology
 
-This Element features DataJoint schemas for analyzing extracellular array electrophysiology data acquired with Neuropixels probes and spike sorted using Kilosort spike sorter. Each Element is a modular pipeline for data storage and processing with corresponding database tables that can be combined with other Elements to assemble a fully functional pipeline.
+This Element features DataJoint schemas for analyzing extracellular array
+electrophysiology data acquired with Neuropixels probes and spike sorted using Kilosort
+spike sorter. Each Element is a modular pipeline for data storage and processing with
+corresponding database tables that can be combined with other Elements to assemble a
+fully functional pipeline.
+
+![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
+
+The Element is comprised of `probe` and `ephys` schemas. Several `ephys` schemas are
+developed to handle various use cases of this pipeline and workflow: 
 
-The Element is comprised of `probe` and `ephys` schemas. Several `ephys` schemas are developed to handle various use cases of this pipeline and workflow: 
 + `ephys_acute`: A probe is inserted into a new location during each session. 
-+ `ephys_chronic`: A probe is inserted once and used to record across multiple sessions. 
-+ `ephys_precluster`: A probe is inserted into a new location during each session. Pre-clustering steps are performed on the data from each probe prior to Kilosort analysis.
-+ `ephys_no_curation`: A probe is inserted into a new location during each session and Kilosort-triggered clustering is performed without the option to manually curate the results. 
 
-Visit the [Concepts page](./concepts.md) for more information about the use cases of `ephys` schemas and an explanation of the tables. To get started with building your own data pipeline, visit the [Tutorials page](./tutorials.md).  
++ `ephys_chronic`: A probe is inserted once and used to record across multiple
+  sessions. 
 
-### `ephys_acute` module
-![element-array-ephys-acute diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
++ `ephys_precluster`: A probe is inserted into a new location during each session.
+  Pre-clustering steps are performed on the data from each probe prior to Kilosort
+  analysis.
 
-### `ephys_chronic` module
-![element-array-ephys-chronic diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_chronic.svg)
++ `ephys_no_curation`: A probe is inserted into a new location during each session and
+  Kilosort-triggered clustering is performed without the option to manually curate the
+  results. 
 
-### `ephys_precluster` module
-![element-array-ephys-precluster diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_precluster.svg)
+Visit the [Concepts page](./concepts.md) for more information about the use cases of
+`ephys` schemas and an explanation of the tables. To get started with building your own
+data pipeline, visit the [Tutorials page](./tutorials.md).