Atlantis Ecosystem Model Wiki

This repository contains the Atlantis Ecosystem Model documentation, converted from Confluence Wiki to a Quarto website.

Live site: https://Atlantis-Ecosystem-Model.github.io/atlantis-wiki/

About

The Atlantis Ecosystem Model is a deterministic biogeochemical whole-of-ecosystem model designed to support ecosystem-based management and marine spatial planning.

Conversion Process

This Quarto site was generated from a Confluence Wiki export using a custom Python conversion script (convert_to_quarto.py). The conversion process involved:

1. HTML to Markdown Conversion

• Parsed Confluence HTML export files using BeautifulSoup
• Converted HTML content to Markdown using the markdownify library
• Preserved page titles, authors, and hierarchical structure

2. Asset Handling

• Attachments: Flattened nested attachment directories (attachments/12345/file.pdf → attachments/file.pdf)
• Equation images: Copied LaTeX equation PNGs from download/export/ to equations/
• Images: Preserved icons and other images

3. Link Fixing

• Converted internal .html links to .qmd links
• Fixed attachment paths to use flattened structure
• Fixed equation image paths (download/export/*.png → equations/*.png)
• Removed problematic Confluence plugin paths (e.g., com.atlassian.confluence.plugins...)

4. Confluence-Specific Element Handling

• Converted Confluence info/warning/tip panels to Quarto callouts
• Extracted LaTeX equations from latexmath-mathblock tables
• Removed emoticon images (replaced with alt text)
• Cleaned up code blocks

Changelog Consolidation

A major enhancement was consolidating version history from multiple scattered sources into a single Changelog page.

Sources Consolidated

The changelog pulls information from these sources:

Source	Content Type
Atlantis-Updates page	Table with Revision, Date, and Content columns (2016-2020)
Atlantis-Bug-Fixes-and-Versions page	Table with Date, Revision, Author, JIRA Issue, and Notes
downloaded_pages/YYYY/Mon/*.html	Individual blog posts organized by year/month (2008-2023)
Redev page	Embedded blog post listings
Changes-made-to-the-input-files page	Embedded blog post listings with inputchanges label

Changelog Features

• Sorted by date (newest first)
• Grouped by year for easy navigation
• Version numbers extracted from content (e.g., "v 6678")
• Deduplicated entries with same version and similar titles
• Full text displayed for entries without dedicated pages
• Linked titles for entries that have dedicated blog post pages (in posts/ folder)

Pages Removed (Consolidated into Changelog)

The following pages were not converted as standalone pages because their content was consolidated into the Changelog:

Original Page	Reason
Atlantis-Updates	Table entries moved to Changelog
Atlantis-Bug-Fixes-and-Versions	Table entries moved to Changelog
Redev	Embedded blog listings moved to Changelog
Changes-made-to-the-input-files	Embedded blog listings moved to Changelog

Blog Posts Converted to Individual Pages

Blog posts from downloaded_pages/ were converted to individual .qmd files in the posts/ folder, with:

• Full content preserved
• Date extracted from metadata or folder structure
• Version number extracted from content
• Author information preserved
• Back-link to Changelog

Data Fixes Applied

During conversion, the following data issues were automatically corrected:

Issue	Fix
Date typo "19/July/12016"	Corrected to "19/July/2016" via regex
Truncated descriptions	Full text preserved for entries without linked pages

Repository Structure

atlantis-wiki/
├── _quarto.yml          # Quarto configuration
├── index.qmd            # Home page
├── changelog.qmd        # Consolidated version history
├── *.qmd                # Converted wiki pages
├── posts/               # Individual blog post pages
│   └── *.qmd
├── attachments/         # PDF, DOCX, PPTX, and other attachments
├── equations/           # LaTeX equation PNG images
├── images/              # Icons and other images
├── styles.css           # Custom CSS
└── .github/
    └── workflows/
        └── publish.yml  # GitHub Actions deployment

Building Locally

Prerequisites

• Quarto (v1.3 or later)
• Python 3.x (only needed if re-running conversion)

Preview

quarto preview

Render

quarto render

The rendered site will be in the _site/ folder.

Re-running the Conversion

If you need to re-convert from the original Confluence export:

Prerequisites

pip install beautifulsoup4 markdownify lxml

Run Conversion

Place convert_to_quarto.py in the Confluence export directory (with the .html files) and run:

python convert_to_quarto.py

This will create/overwrite the quarto_site/ folder.

Deployment

This site is automatically deployed to GitHub Pages via GitHub Actions when changes are pushed to the main branch.

License

The Atlantis Ecosystem Model documentation is maintained by CSIRO. See the original Confluence Wiki for licensing information.

Credits

• Original Wiki: CSIRO Atlantis Team (Beth Fulton, Bec Gorton, and contributors)
• Conversion: Automated conversion script developed with assistance from Claude (Anthropic)