Hotfix from master

Merge branch 'master' into SharedDevelopment

Incorporates documentation and action fixes.

Author: stiber

.github/workflows/tests.yml

@@ -1,11 +1,20 @@
 name: Unit and Regression Tests
-
+# Any changes made to documentation won't trigger tests.
 on:
   push:
     branches: [ master,development ]
+    paths-ignore:
+      - '.github/**'       # Ignore .github folder
+      - '**/Doxyfile'      # Ignore changes to Doxygen config
+      - 'docs/**'          # Ignore documentation folder
+      - '*.md'             # Ignore Markdown files
   pull_request:
     types: [opened, synchronize, reopened]
-
+    paths-ignore:
+      - '.github/**'       # Ignore .github folder
+      - '**/Doxyfile'      # Ignore changes to Doxygen config
+      - 'docs/**'          # Ignore documentation folder
+      - '*.md'             # Ignore Markdown files
 defaults: 
   run:
     working-directory: build

docs/Developer/GHActions.md

@@ -10,6 +10,9 @@ This action is Triggered on a monthly schedule. At the first of every month the
 
 The manual GitHub Pages action is a feature that came from wanting to quickly publish changes to documentation files in our docs folder. This action is activated by navigating to the actions tab, selecting the "Publish GitHub Pages Manually" workflow, then toggling the run workflow button on the desired branch. The branch to run this action on will typically be the master branch as that is the one with the most up to date documentation. Once toggled, it will take the docs files from the selected branch and publish them to the gh-pages branch as a forced orphan just like in the gh-pages.yml workflow. This action will also regenerate the Doxygen files in the same way the gh-pages.yml script does. This is done because other branches doesn't hold the Doxygen/html files and would lose this information if not regenerated during this script.
 
+### Mermaid Diagrams _config.yml
+Since mermaid is set to `true` in _config.yml, anytime GitHub Pages action is triggered, _includes/head-custom.html uses Javascript to seek for any files that contains `mermaid` (once webpage finishes loading), then loads mermaid library.
+
 ## PlantUML Action plantUML.yml
 
 The plantUML action occurs anytime a plantUML file is modified or added during a pull request or a push to the master branch. These .puml files are supposed to be located in the UML folder within the Developer folder. This action starts by checking out the repository using [actions/checkout](https://github.com/actions/checkout) with a fetch depth of 0. The next step is to grab all of the .puml files that need to be turned into images. This is done by using a basic bash command to grab all .puml files which is then piped into an awk script to parse out the unnecessary files and construct an output string with all the necessary files. The output string will look like so: "file1.puml file2.puml file3.puml file4.puml\n". This output string is then confirmed by an echo command which prints out the string to the actions terminal. Next, the .png and .svg files are generated from the .puml files in the output string using a fork of [holowinski/plantuml-github-action]. These files are placed within the diagrams folder located within the UML folder. Lastly, the local changes are committed then pushed to the remote repository using [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action).

docs/Developer/GHPages.md

@@ -27,6 +27,8 @@ You can find more on the automation of the publication by navigating to the [Git
 
 All documents used for our pages reside in the docs folder within the Graphitti repo.
 
+`_includes` folder contains `head-custom.html`, which is resposnible for generating Mermaid diagrams. (More info here: [GHActions.md](GHActions.md#mermaid-diagrams-_configyml))
+
 The Developer folder is used for documentation that deals with documenting systems for developers of Graphitti.
 
 The Doxygen folder is used for documentation that refers to the Doxygen system.

docs/_config.yml

@@ -3,5 +3,5 @@ theme: jekyll-theme-slate
 title: Graphitti
 description: A project to facilitate construction of high-performance neural simulations
 
-
-show_downloads: false
+mermaid: true
+show_downloads: false

docs/_includes/head-custom.html

@@ -0,0 +1,22 @@
+{% if site.mermaid %}
+<script type="module">
+
+    // Old and unoptimized. 
+    // Injects mermaid into each page regardless if a page uses it or not
+    // Array.from(document.getElementsByClassName("language-mermaid")).forEach(element => {
+    //   element.classList.add("mermaid");
+    // });
+    // import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@11/dist/mermaid.esm.min.mjs';
+    // mermaid.initialize({ startOnLoad: true });
+
+    // Latest version as of 1/7/26
+    import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@11/dist/mermaid.esm.min.mjs';
+    
+    mermaid.initialize({ startOnLoad: false });
+    
+    // Once page is loaded, render Mermaid diagrams
+    document.addEventListener('DOMContentLoaded', () => {
+    mermaid.run({ querySelector: '.language-mermaid' });
+    });
+</script>
+{% endif %}

docs/index.md

@@ -14,7 +14,7 @@
 
 2. [Developer Documentation](Developer/index.md)
 
-   2.1 [GitFlow Documentation](Developer/GitFlowDiagram.md)
+   2.1 [GitFlow Documentation](Developer/GitFlow.md)
 
    2.2 [Code Formatting Etiquettes](Developer/codingConventions.md)
 
@@ -52,4 +52,4 @@ Those who have helped make Graphitti what it is and shaping what it will be.
 [//]: # (Moving URL links to the bottom of the document for ease of updating - LS)
 [//]: # (Links to repo items which exist outside of the docs folder need a direct link.)
 
-[Code of Conduct]: <https://github.com/UWB-Biocomputing/Graphitti/blob/master/CODE_OF_CONDUCT.md>
+[Code of Conduct]: <https://github.com/UWB-Biocomputing/Graphitti/blob/master/CODE_OF_CONDUCT.md>