Merge branch 'main' of https://github.com/datajoint-company/datajoint-docs

Author: dimitri-yatsenko

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+#
+ignore-words-list = shepard

.docker/Dockerfile

@@ -8,7 +8,7 @@ RUN \
     rm ${PIP_REQUIREMENTS} && \
     rm ${APK_REQUIREMENTS}
 RUN \
-    pip install --no-cache git+https://${GITHUB_TOKEN}@github.com/guzman-raphael/mkdocs-material-insiders.git@master || \
+    pip install --no-cache git+https://${GITHUB_TOKEN}@github.com/datajoint/mkdocs-material-insiders.git@master || \
     echo "using public mkdocs-material..."
 COPY --chown=anaconda:anaconda ./mkdocs.yaml /main/mkdocs.yaml
 COPY --chown=anaconda:anaconda ./src /main/src

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+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@v2

mkdocs.yaml

@@ -2,8 +2,8 @@
 
 site_name: DataJoint Documentation
 site_url: http://localhost/docs
-repo_name: datajoint-company/datajoint-docs
-repo_url: https://github.com/datajoint-company/datajoint-docs
+repo_name: datajoint/datajoint-docs
+repo_url: https://github.com/datajoint/datajoint-docs
 nav:
   - Welcome: index.md
   - DataJoint Python: core/datajoint-python/

src/additional-resources.md

@@ -21,7 +21,7 @@ A collection of additional open-source tools for building and operating scientif
 
     A REST API server for interacting with DataJoint pipelines.
 
-    :octicons-arrow-right-24: [Legacy docs](https://datajoint.com/docs/core/pharus) | 
+    :octicons-arrow-right-24: [Docs](https://datajoint.com/docs/core/pharus) | 
     [Source code](https://github.com/datajoint/pharus/)
 
 </div>

src/elements/concepts.md

@@ -45,7 +45,7 @@ schemas: `scan` and `imaging`.
 The following YouTube videos provide information on basic design principles and file organization.
 
 - [Why neuroscientists should use relational databases](https://www.youtube.com/watch?v=q-PMUSC5P5o)
-  compared to traditional file heirarchies.
+  compared to traditional file hierarchies.
 - [Quickstart Guide](https://www.youtube.com/watch?v=5R-qnz37BKU) including 
   terminology, and how to read DataJoint Diagrams and DataJoint Python table 
   definitions.

src/elements/index.md

@@ -35,7 +35,7 @@ Below are the projects that make up the family of open-source DataJoint Elements
     A data pipeline for Neuropixels probes.
 
     [:octicons-arrow-right-24: Interactive tutorial on GitHub
-    Codespaces](https://github.com/datajoint/workflow-array-ephys#interactive-tutorial){:target="_blank"}
+    Codespaces](https://github.com/datajoint/element-array-ephys#interactive-tutorial){:target="_blank"}
 
     [:octicons-arrow-right-24: Docs](./element-array-ephys/)
 
@@ -74,6 +74,9 @@ Below are the projects that make up the family of open-source DataJoint Elements
 
     A data pipeline for pose estimation with DeepLabCut.
 
+    [:octicons-arrow-right-24: Interactive tutorial on GitHub
+    Codespaces](https://github.com/datajoint/element-deeplabcut#interactive-tutorial){:target="_blank"}
+
     [:octicons-arrow-right-24: Docs](./element-deeplabcut/)
 
 -   :fontawesome-brands-python:{ .lg .middle } **Element Facemap**

src/elements/user-guide.md

@@ -74,7 +74,7 @@ following the install instructions.
 
 ### Conda
 
-Python projects each rely on different depenencies, which may conflict across projects.
+Python projects each rely on different dependencies, which may conflict across projects.
 We recommend working in a Conda environment for each project to isolate the
 dependencies. For more information on why Conda, and setting up the version of Conda
 that best suits your needs, see 
@@ -157,7 +157,7 @@ instructions on Jupyter within VS Code).
     conda install jupyter ipykernel nb_conda_kernels
     ```
 
-2. Ensure your VS Code python intepreter is set to your Conda environment path.
+2. Ensure your VS Code python interpreter is set to your Conda environment path.
    
     <details> <!-- Can't use `??? Note` format within list  -->
     <summary>Click to expand more details.</summary>
@@ -546,7 +546,7 @@ organized, and how some files are named.
         
     - The paths in your various `yaml` files reflect the current folder structure.
 
-    - You have generated thge `pickle` and `mat` training files. If not, follow the 
+    - You have generated the `pickle` and `mat` training files. If not, follow the 
         DeepLabCut guide to 
         [create a training dataset](https://github.com/DeepLabCut/DeepLabCut/blob/master/docs/standardDeepLabCut_UserGuide.md#f-create-training-datasets)
 
@@ -579,7 +579,7 @@ organized, and how some files are named.
 ## Relational databases
 
 DataJoint helps you connect to a database server from your programming environment 
-(i.e., Python or MATLAB), granting a number of benefits over traditional file heirarchies 
+(i.e., Python or MATLAB), granting a number of benefits over traditional file hierarchies 
 (see [YouTube Explainer](https://www.youtube.com/watch?v=q-PMUSC5P5o)). We offer two 
 options:
 
@@ -681,9 +681,9 @@ depending on your needs.
 
 ### Central Database
 
-To set up a detabase on dedicated hardware may require expertise to set up and maintain.
+To set up a database on dedicated hardware may require expertise to set up and maintain.
 DataJoint's [MySQL Docker image project](https://github.com/datajoint/mysql-docker) 
-provides all the informaiton required to set up a dedicated database.
+provides all the information required to set up a dedicated database.
 
 ## Interacting with the Workflow
 

src/index.md

@@ -30,13 +30,12 @@
      [:octicons-arrow-right-24: Learn
      more](https://datajoint.com/works){:target="_blank"} | [Sign-in](https://works.datajoint.com){:target="_blank"}
 
--   **Research projects supported by DataJoint**
+-   **Project Showcase**
 
      ---
 
-     Projects and research teams using DataJoint Python, DataJoint Elements, or 
-     DataJoint Works
+     Projects and research teams supported by DataJoint software
 
-     [:octicons-arrow-right-24: Project Showcase](projects/index.md)
+     [:octicons-arrow-right-24: Learn more](projects/index.md)
 
 </div>

src/projects/teams.md

@@ -1,5 +1,5 @@
 <!-- markdownlint-disable MD013 -->
-# Projects <!-- 74 -->
+# Projects
 
 DataJoint was originally developed by working systems neuroscientists at Baylor College
 of Medicine to meet the needs of their own research. Below is a partial list of known teams who use DataJoint.
@@ -17,7 +17,7 @@ of Medicine to meet the needs of their own research. Below is a partial list of
   + Princeton<a href="https://www.braincogs.org/" target="_blank"> BRAIN CoGS</a> (<a href="https://github.com/braincogs/" target="_blank">GitHub</a>)
   + Rochester-NYU-Harvard<a href="https://causalityinmotion.github.io/team.html" target="_blank"> Neural basis of causal inference</a>
 
-## Individual Labs and Researchers <!-- 64 -->
+## Individual Labs and Researchers <!-- 67 -->
 
 + Allen Institute
   + <a href="https://alleninstitute.org/what-we-do/brain-science/research/mindscope-program/" target="_blank">Mindscope Program</a>
@@ -54,6 +54,9 @@ of Medicine to meet the needs of their own research. Below is a partial list of
   + <a href="https://smirnakislab.bwh.harvard.edu/" target="_blank">Stelios Smirnakis Lab</a>
 + Indiana University
   + <a href="http://www.lulaboratory.com/" target="_blank">Lu Lab</a>
++ Janelia Research Campus
+  + <a href="https://www.janelia.org/lab/dennis-lab" target="_blank">Emily Dennis Lab</a>
+  + <a href="https://www.janelia.org/lab/koay-lab" target="_blank">Sue Ann Koay Lab</a>
 + Johns Hopkins University
   + <a href="https://www.jhuapl.edu/" target="_blank">Applied Physics Lab</a> (<a href="https://github.com/aplbrain" target="_blank">GitHub</a>)
 + Kavli Institute for Systems Neuroscience
@@ -63,9 +66,9 @@ of Medicine to meet the needs of their own research. Below is a partial list of
   + <a href="https://www.neuro.bio.lmu.de/research_groups/res-katzner/index.html" target="_blank">Katzner Lab</a>
 + MIT
   + <a href="https://www.wanglab-neuro.org" target="_blank">Fan Wang Lab</a>
-+ National Institutes Health
++ National Institutes of Health
   + <a href="http://ericthomson.net/" target="_blank">Eric E. Thomson</a>
-  + Joshua Gordon Lab / David Kupferschmidt 
+  + <a href="https://research.ninds.nih.gov/staff-directory/joshua-gordon-md-phd" target="_blank">Joshua Gordon Lab / David Kupferschmidt</a>
 + New York University
   + <a href="https://angelakilabnyu.org/" target="_blank">Dora Angelaki Lab</a>
 + New York University Langone Medical Center