Knowledge Library — The Phoenix Chronobiology Projects

⚠️ This repository/site is no longer active. It's content has been incorporated into the parent site, The Phoenix Chronobiology Projects, under the Reading Room menu item.

Overview

The Phoenix Chronobiology Projects:

• Work with the University of Minnesota's Halberg Chronobiology Center.
• Operate as a study group of the Twin Cities Section of the Institute of Electrical and Electronics Engineers.

The goals of the Projects are to develop:

1. An ambulatory blood pressure monitor that is inexpensive, unobtrusive, easy to use, and collects a week of blood pressure measurements.
2. A platform for biorythm analysis.

The Halberg Chronobiology Center wants the monitor and analytic framework for long term use on massive scale for:

1. Assessing cardiovascular health, detecting pre-disease early, and optimizing treatment schedules, in order to reduce the number of people who die of preventable heart attacks and strokes.
2. Understanding, for health surveillance and maintenance, how blood pressure and heart rate vary in response to stimuli in everyday life.

This repository

The Library is an indexed collection of papers and slides about topics that are important to The Phoenix Chronobiology Projects. These include:

• Publications and research materials written by members of the project.
• Reference materials used by the project.

This repository is built as a subproject/subcomponent of The Phoenix Chronobiology Projects site.

Static site generator

MkDocs is a static site generator that is geared toward building project 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.

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
    articles/           # The equivalent of library catalog cards
    files/              # Locally archived knowledge assets
    images/
    javascripts/
    stylesheets/
    ...                 # Other markdown pages and other files

Note that most articles/cards will link to local works, archived in files. 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).

Theme

Material for MkDocs

Markdown Front-Mmatter

To index its articles, the library uses Material for MkDocs built-in Blog plugin. The plugin uses markdown front-matter to automatically generate views of the content in folder articles. The views are listed in generated website's left-hand navigation panel.

---
date:
  created: 2009-10-01
  updated: 2024-10-15
categories:
  - Manuscripts
---
# Paper Title Number 1

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

See Material for MkDocs → plugins → blog.

Building the site

Production build

The site is built and deployed via GitHub Actions.

The actions are triggered by a git push to the main branch.

The repository currently places minimal constraints on change. Anyone with write access may directly push content from a local repository to the GitHub repository. Expect more robust change management as the number of contributors grows.

Local build

1. Set up git

   See https://git-scm.com/downloads

2. Checkout repository

   git clone https://github.com/phoenix-chronobiology/phoenix-biorhythm-platform.git
   

3. Set up Node.js runtime

   Production environment includes Node version 20.x

   See https://nodejs.org/en

4. Set up Node.js dependencies

   npm clean-install
   

5. Set up Python runtime

   Production environment includes Python version 3.x

   See https://www.python.org/

6. Install Python dependencies

   pip install mkdocs
   pip install mkdocs-material
   pip install mkdocs-macros-plugin
   pip install mkdocs-git-revision-date-localized-plugin
   pip install mkdocs-link-marker
   pip install mkdocs-exclude
   

7. Build documentation

   mkdocs build --clean
   mkdocs --version
   

8. Start MkDocs server

   See mkdocs serve -h for port options

   Default is port 8000

   mkdocs serve
   

9. Open local site

   Use port specified with mkdocs serve command

   Open http://127.0.0.1:8000/