About the site

Host

The Phoenix Projects operate as a study group of the Twin Cities Section of the Institute of Electrical and Electronics Engineers ⧉.

The Phoenix Biorhythm site is hosted on GitHub Pages.

Static Site Generator

MkDocs is a static site generator that's geared towards building project documentation. Documentation source files are written primarily in Markdown ⧉, and configured with a single YAML configuration file

This site uses Markdown, HTML and cascading style sheets.

For full documentation, visit mkdocs.org ⧉.

MkDocs Commands

• mkdocs new [dir-name] - Create a new project.
• mkdocs serve - Start the live-reloading docs server.
• mkdocs build - Build the documentation site.
• mkdocs -h - Print help message and exit.

Project layout

mkdocs.yml              # The configuration file
docs/
    index.md            # The documentation homepage
    about/
        index.md
        images/         # subproject-specific images
        ...
    abpm/               # ambulatory blood pressure monitor subproject
        index.md
        images/         # subproject-specific images
       ...
    algorithms/         # biorhythm analysis algorithms subproject
        index.md
        images/         # subproject-specific images
        ...
    biorhythm-platform/ # biorhythm analysis platform subproject
        index.md
        images/         # subproject-specific images
        architecture/
            index.md
            ...
        privacy-security/
            index.md
            ...
        requirements/
            index.md
            ...
    glossary/
        index.md
        images/         # glossary-specific images
    images/             # program-general images, icons and clip art     
    javascripts/
    reading-room/
        posts/          # blog posts & the equivalent of library catalog cards
        files/          # locally archived knowledge assets
        images/
        index.md
        .authors.yml
    snippets/
    stylesheets/
    ...                 # Other markdown pages and other files

Theme

Material for MkDocs ⧉

Macros

See macros info

Typography

Material for MkDocs directly integrates with Google Fonts ⧉. All fonts are taken from that collection.

Body text and titles are set in , a nonserif font.

Code samples are set in , a nonserif, monospace font.

For clients who do not have these fonts, the style sheets specify some standard alternatives.

See also "Privacy".

Palette

The site provides both light and dark color schemes:

Mode	Color Scheme
Light	MkDocs default
Dark	MkDocs slate

The primary color is set to blue-grey (#546d78).

The accent color is set to indigo (#4051b5).

Graphics

Image	Explanation	Source
	The Phoenix Projects mark symbolizes the investigation of variation in blood pressure.	The Phoenix is a composite of the following three images.
	The interior of a human heart and some of the blood vessels	SERVIER MEDICAL ART, a service to medicine provided by Les Laboratoires Servier www.servier.com ⧉. Image retrieved from https://smart.servier.com/wp-content/uploads/2016/10/coeur_01.png ⧉. Servier Medical Art is licensed under CC BY 4.0
	Magnifying glass	"Magnifying Glass", by deelight ⧉, on OPENCLIPART.org ⧉.
	An abstract: electrocardiogram (ECG) tracing in lime green (#33cc33) An abstract atrial blood pressure cycle in persian red (#cc3333) The tracings are drawn along the same timescale.	Derived from the image titled "Timing of arterial pulse and the ECG", in "Normal arterial line waveforms", Deranged Physiology: A free online resource for Intensive Care Medicine ⧉, by Alex Yartsev ⧉. The derivation removed all but the waveforms and converted the result to SVG.
	The Phoenix Logo incorporates the Phoenix Mark.
		The favicon is "circadian rhythms" by bsd studio from Noun Project ⧉ (CC BY 3.0). The same image is used for the apple-touch-icon.

The hero image on the site's home page is the Phoenix Projects mark with CCS animation added to the waveforms.

Math Notation

Math statements are rendered with the LaTex ⧉ typesetting language, using the MathJax ⧉ library for displaying mathematical content in browsers. MathJax is incorporated into MkDocs using arithmatex ⧉, a Python Markdown extension.

Reading Room

The Reading Room is constructed with the Blog plug-in built into Material for MkDocs ⧉. The Blog plug-in uses Markdown front-matter to automatically create:

1. Archive pages that each list a subset of assets for a time interval.
2. Category pages that each list a subset of assets for each category.

Catagories include but are not limited to:

1. Conferences
2. Manuscripts
3. Project Meetings
4. Project Process

Sample from Project Meetings

---
date:
  created: 2024-04-24
  updated: 2024-10-15
categories:
  - Project Meetings
---

# Welcome 2024!

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod
tempor incididunt ut labore et dolore magna aliqua.

A given item can be assigned to multiple categories.

Each manuscript particularly has a page that is written in Markdown and that serves as library index card. The card includes:

1. The work's title.
2. The work's authors.
3. An abstract or excerpt of the work.
4. The date of distribution or publication.
5. The categories to which the projects assign the work.
6. A citation to the work.
7. URLs to the digital files comprising the asset. The work may consist of some combination of papers, slides, spreadsheets, or graphics.

The URLs usually point into this site's source GitHub repository. However, a card may contain a link into:

• A GitHub repository of an individual project contributor;
• The GitHub repository for Hyde ⧉, the archive of The Phoenix Chronobiology Projects' legacy site; or
• The home site of the project sponsor, the University of Minnesota's Halberg Chronobiology Center, https://halbergchronobiologycenter.umn.edu) ⧉.

Sample from Manuscripts

---
title: "Paper Title Number 1"
date:
  created: 2009-10-01
  updated: 2024-10-15
categories:
  - Manuscripts
citation: 'Your Name, You. (2009). &quot;Paper Title Number 1.&quot; <i>Journal 1</i>. 1(1).'
paperurl: '../files/paper1.pdf'
slidesurl: '../files/slides1.pdf'
bibtexurl: '../files/bibtex1.bib'
---
# About the Site

![prototype banner](../../images/prototype-color.png){ width="100" align="right" } 

The contents above will be part of a list of publications, if the user clicks the link for the publication than the contents of section will be rendered as a full page, allowing you to provide more information about the paper for the reader. When publications are displayed as a single page, the contents of the above "citation" field will automatically be included below this section in a smaller font.
<!-- more -->

/// details | :material-library: 
    open: true
**Recommended citation**: {{ citation }}

[Download Paper]({{ paperurl }}) | [Download Slides]({{ slidesurl }}) | [Download Bibtex]({{ bibtexurl }})
///

This ability to reference sources outside the site is influenced by the activation of the Privacy plug-in.

IDEA

1. The project must decide whether to govern the list of categories to avoid redundant or misunderstood keywords.
2. The plug-in can highlight the authors of each article. However, just as for the Blog, the project must still resolve details about author privacy. Keep in mind that, even if authors are highlighted, an index of posts by author is not generated, unlike the Archive and Category pages.
3. The summary pages (Archive, Category) are similar to those implemented by Academic Pages ⧉. Because Academic Pages uses Jekyll ⧉ rather than MkDocs ⧉ for static site generation, the templates for Academic Pages would need converting from Liquid ⧉ to Jinja ⧉. (The grammar and environments of Liquid and Jinja are similar, so the conversion would be straightforward.)

Privacy

The site uses the privacy plugin built into Material for MkDocs ⧉. The plugin:

1. Scans the generated HTML for external assets, such as scripts, style sheets, images, and web fonts.
2. Downloads them.
3. Stores them in the site directory.
4. Replaces all references with links to the downloaded copies for self-hosting.

License

Tip

The following site, provided by GitHub, is recommended for picking an open source license.

https://choosealicense.com ⧉.

This work is licensed under Creative Commons Attribution 4.0 International Public License.

This license is intended for documentation and media only. It is not intended for any software or hardware described on this site.