Merge pull request #89 from datajoint/update-in-docs-url

feat: ✨ update url reference from datajoint.com/docs/ to docs.datajoint.com | fix: element user guild mermaid chart

Author: kushalbakshi

README.md

@@ -1,7 +1,6 @@
 # DataJoint Documentation
 
-This is the home for DataJoint software documentation as hosted at https://datajoint.com/docs
-
+This is the home for DataJoint software documentation as hosted at https://docs.datajoint.com
 ## VSCode Linter Extensions and Settings
 
 The following extensions were used in developing these docs, with the corresponding
@@ -39,7 +38,7 @@ Then install the required packages:
 pip install -r pip_requirements.txt
 ```
 
-Run mkdocs at: http://127.0.0.1:8000/docs/
+Run mkdocs at: http://127.0.0.1:8000/
 ```bash
 # It will automatically reload the docs when changes are made
 mkdocs serve --config-file ./mkdocs.yaml
@@ -57,7 +56,7 @@ Then run the following:
 MODE="LIVE" docker compose up --build
 ```
 
-Navigate to http://127.0.0.1:8000/docs/ to preview the changes.
+Navigate to http://127.0.0.1:8000/ to preview the changes.
 
 This setup supports live-reloading so all that is needed is to save the markdown files
 and/or `mkdocs.yaml` file to trigger a reload.
@@ -77,10 +76,9 @@ INFO    -  Doc file 'index.md' contains an unrecognized relative link './core/da
   - You hit `datajoint.com/*` on your browser
   - It'll bring you to the reverse proxy server first, that you wouldn't notice
   - when your URL ends with:
-    - `/` is the company page
-    - `/docs/` is the landing/navigation page hosted by datajoint/datajoint-docs's github pages
-    - `/docs/core/datajoint-python/` is the actual docs site hosted by datajoint/datajoint-python's github pages
-    - `/docs/elements/element-*/` is the actual docs site hosted by each element's github pages
+    - `/` is the landing/navigation page hosted by datajoint/datajoint-docs's github pages
+    - `/core/datajoint-python/` is the actual docs site hosted by datajoint/datajoint-python's github pages
+    - `/elements/element-*/` is the actual docs site hosted by each element's github pages
 
 
 ```log

docker-compose.yaml

@@ -1,6 +1,6 @@
 # MODE="LIVE|BUILD" docker compose up --build
 #
-# Navigate to http://localhost/docs/
+# Navigate to http://localhost:8000/
 services:
   docs:
     # image: datajoint/datajoint-docs

mkdocs.yaml

@@ -71,6 +71,7 @@ theme:
         name: Switch to light mode
 plugins:
   - search
+  - mermaid2
   - section-index
   # There is no welcome.md anymore
   # - redirects:
@@ -96,7 +97,7 @@ markdown_extensions:
       custom_fences:
         - name: mermaid
           class: mermaid
-          format: !!python/name:pymdownx.superfences.fence_code_format
+          format: !!python/name:mermaid2.fence_mermaid_custom
   - pymdownx.tabbed:
       alternate_style: true
   - footnotes

pip_requirements.txt

@@ -4,4 +4,5 @@ mkdocs-exclude
 mdx_truly_sane_lists
 mkdocs-pymdownx-material-extras
 pymdown-extensions
-mkdocs-section-index
+mkdocs-section-index
+mkdocs-mermaid2-plugin

src/additional-resources.md

@@ -12,7 +12,7 @@ A collection of additional open-source tools for building and operating scientif
 
     A MATLAB client for defining, operating, and querying data pipelines.
 
-    :octicons-arrow-right-24: [Legacy docs](https://docs.datajoint.org/matlab/) | 
+    :octicons-arrow-right-24: [Legacy docs](https://datajoint.github.io/datajoint-docs-original/matlab/) | 
     [Source code](https://github.com/datajoint/datajoint-matlab)
 
 -   :fontawesome-solid-flask:{ .lg .middle } **DataJoint Pharus**
@@ -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: [Docs](https://datajoint.com/docs/core/pharus) | 
+    :octicons-arrow-right-24: [Docs](https://docs.datajoint.com/core/pharus) | 
     [Source code](https://github.com/datajoint/pharus/)
 
 </div>
@@ -36,8 +36,7 @@ A collection of additional open-source tools for building and operating scientif
 
     A browser-based graphical user interface for data entry and navigation. 
 
-    :octicons-arrow-right-24: [Legacy 
-    docs](https://datajoint.com/docs/core/datajoint-labbook/) | 
+    :octicons-arrow-right-24: [Legacy docs](https://datajoint.github.io/datajoint-labbook/) | 
     [Source code](https://github.com/datajoint/datajoint-labbook/)
 
 -   :fontawesome-brands-chrome:{ .lg .middle } **DataJoint SciViz**
@@ -46,7 +45,7 @@ A collection of additional open-source tools for building and operating scientif
 
     A framework for making low-code web apps for data visualization.
 
-    :octicons-arrow-right-24: [Legacy docs](https://datajoint.com/docs/core/sci-viz/) | 
+    :octicons-arrow-right-24: [Docs](https://docs.datajoint.com/core/sci-viz/) | 
     [Source code](https://github.com/datajoint/sci-viz)
 
 </div>
@@ -78,8 +77,7 @@ graph
     ---
     MySQL server configured to work with DataJoint.
 
-    :octicons-arrow-right-24: [Docker 
-    image](https://hub.docker.com/r/datajoint/mysql) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/mysql) | 
     [Source code](https://github.com/datajoint/mysql-docker)
 
 -   :fontawesome-brands-docker:{ .lg .middle } **datajoint/miniconda3**
@@ -88,8 +86,7 @@ graph
 
     Minimal Python Docker image with [conda](https://docs.conda.io/en/latest/).
 
-    :octicons-arrow-right-24: [Docker
-    image](https://hub.docker.com/r/datajoint/miniconda3) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/miniconda3) | 
     [Legacy docs](https://datajoint.github.io/miniconda3-docker/) | 
     [Source code](https://github.com/datajoint/miniconda3-docker)
 
@@ -99,8 +96,7 @@ graph
 
     Minimal base Docker image with DataJoint Python dependencies installed. 
 
-    :octicons-arrow-right-24: [Docker 
-    image](https://hub.docker.com/r/datajoint/djbase) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djbase) | 
     [Legacy docs](https://datajoint.github.io/djbase-docker/) | 
     [Source code](https://github.com/datajoint/djbase-docker)
 
@@ -110,8 +106,7 @@ graph
 
     Docker image for running tests related to DataJoint Python. 
 
-    :octicons-arrow-right-24: [Docker 
-    image](https://hub.docker.com/r/datajoint/djtest) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djtest) | 
     [Legacy docs](https://datajoint.github.io/djtest-docker/) | 
     [Source code](https://github.com/datajoint/djtest-docker)
 
@@ -121,8 +116,7 @@ graph
 
     Official DataJoint Docker image.
 
-    :octicons-arrow-right-24: [Docker
-    image](https://hub.docker.com/r/datajoint/datajoint) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/datajoint) | 
     [Source code](https://github.com/datajoint/datajoint-python)
 
 -   :fontawesome-brands-docker:{ .lg .middle } **datajoint/djlab**
@@ -131,9 +125,7 @@ graph
 
     Docker image optimized for running a JupyterLab environment with DataJoint Python. 
 
-    :octicons-arrow-right-24: [Docker 
-    image](https://hub.docker.com/r/datajoint/djlab) | 
-    [Legacy docs](https://datajoint.github.io/djlab-docker/) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djlab) | 
     [Source code](https://github.com/datajoint/djlab-docker)
 
 -   :fontawesome-brands-docker:{ .lg .middle } **datajoint/djlabhub**
@@ -143,9 +135,7 @@ graph
     Docker image optimized for deploying to JupyterHub a JupyterLab environment with 
     DataJoint Python. 
 
-    :octicons-arrow-right-24: [Docker 
-    image](https://hub.docker.com/r/datajoint/djlabhub) | 
-    [Legacy docs](https://datajoint.github.io/djlabhub-docker/) | 
+    :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djlabhub) | 
     [Source code](https://github.com/datajoint/djlabhub-docker)
 
 </div>

src/elements/management/dissemination.md

@@ -5,7 +5,7 @@
 We conduct activities to disseminate Resource components for adoption in diverse
 neuroscience labs. These activities include
 
-- A central [website](https://datajoint.com/docs/elements/) for the Resource.
+- A central [website](https://docs.datajoint.com/elements/) for the Resource.
 - [Conference talks, presentations, and workshops](../../support-events.md)
 - Publications in peer-reviewed journals
 - White papers posted on internet resources and websites

src/elements/user-guide.md

@@ -42,27 +42,20 @@ This diagram describes the general components for a local DataJoint environment.
 
 ```mermaid
 flowchart LR
-  py_interp  -->|DataJoint| db_server[("Database Server\n(e.g., MySQL)")]
-  subgraph conda["Conda environment"]
-    direction TB
-    py_interp[Python Interpreter]
-  end
-  subgraph empty1[" "] %% Empty subgraphs prevent overlapping titles
-    direction TB
-    style empty1 fill:none, stroke-dasharray: 0 1
-    conda
-  end
-  subgraph term["Terminal or Jupyter Notebook"]
-    direction TB
-    empty1
-  end
-  subgraph empty2[" "] %% Empty subgraphs prevent overlapping titles
-    direction TB
-    style empty2 fill:none, stroke-dasharray: 0 1
-    term
-  end
-  class py_interp,conda,term,ide,db_server,DataJoint boxes;
-  classDef boxes fill:#ddd, stroke:#333;
+  %% Nodes
+  py_interp["Python Interpreter"]
+  db_server["Database Server<br>(e.g., MySQL)"]
+  conda_env["Conda Environment"]
+  terminal["Terminal or Jupyter Notebook"]
+
+  %% Edges
+  py_interp -->|DataJoint| db_server
+  terminal --> conda_env
+  conda_env --> py_interp
+
+  %% Styling
+  classDef boxes fill:#ddd,stroke:#333;
+  class py_interp,db_server,conda_env,terminal boxes;
 ```
 
 ### Python

src/partnerships/dandi.md

@@ -20,9 +20,9 @@ integration and interoperability across the two ecosystems.
 
 ### DataJoint
 
-**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of
+**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of
   open-source reference database schemas and analysis workflows for neurophysiology
-  experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an
+  experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an
   open-source software framework. The project is funded by the NIH grant U24 NS116470
   and led by Dr. Dimitri Yatsenko.
 

src/partnerships/facemap.md

@@ -20,9 +20,9 @@ across the two ecosystems.
 
 ### DataJoint
 
-**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of
+**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of
   open-source reference database schemas and analysis workflows for neurophysiology
-  experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an
+  experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an
   open-source software framework. The project is funded by the NIH grant U24 NS116470
   and led by Dr. Dimitri Yatsenko.
 

src/partnerships/nwb.md

@@ -20,9 +20,9 @@
 
 ### DataJoint
 
-**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of
+**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of
   open-source reference database schemas and analysis workflows for neurophysiology
-  experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an
+  experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an
   open-source software framework. The project is funded by the NIH grant U24 NS116470
   and led by Dr. Dimitri Yatsenko.