About

This repo holds the files used for a website exhibiting part of my fossils collection. The site can be accessed at apolithomata.com

Files documentation

images/

Contains the images used in the website.

journal/

Contains handwritten journal entries documenting research, experiments, and conservation work. Includes:

entries/

Markdown files with journal entries in multiple languages (denoted by -EL, -EN, -GRC suffixes).

media/

Images and media files accompanying journal entries.

index.html / index-.html

Auto-generated index page for the journal.

Individual entry pages (auto-generated)

HTML pages for each journal entry in multiple language versions.

jsondata/

Contains .json files that contain static data:

dict.json

Dictionary of terms common to all pages. Manually maintained.

geochronology.json

Contains structured data about fossil localities used in the site. Manually maintained.

pages.json

Auto-generated by pyscripts/generate_pages_json.py. Contains the titles and paths to pages in tree/, used by the search script in header.js.

samples_info.json

Information about fossil samples displayed in the site, such as locality, image samples and their descriptions, etc. Manually maintained.

taxonomy.json

A taxonomic tree of taxon pages contained in the website. It also contains metadata such as whether a taxon is extinct, and their descriptions. Manually maintained

localities/

A directory containing auto-generated pages describing the paleoenvironment at different localities.

pyscripts/

Contains utility python scripts.

site_generator/

templates/

Jinja templates for generating html pages and accompanying .json files.

index.html.template / index.json.template

Templates for generating the homepage.

journal_entry.html.template

Template for generating individual journal entry pages.

journal_index.html.template

Template for generating the journal index page.

locality.html.template / locality.json.template

Templates for generating locality pages.

map.html.template / map.json.template

Templates for generating the map page.

taxon.html.template / taxon.json.template

Templates for generating taxonomic pages.

random-sample.js.template

Template for generating the random sample selection script.

generate_site.py

Executable that will generate all auto-generated content for the website. This includes:

• files under localities/
• files under tree/
• files under journal/
• unclassified.html + unclassified.json
• jsondata/pages.json (generated by invoking ../generate_pages_json.py)
• scripts/random-sample.js (contains an auto-generated list of all samples in the site)
• map.html + map.json

build_journal.py

Builds the journal section from markdown files under journal/entries/. Processes handwritten entries in multiple languages.

sitemap_generator.py

Generates the sitemap.xml file for SEO purposes.

generate_pages_json.py

Navigates the tree/ and creates entries for each page it encounters, then stores the results in jsondata/pages.json. Should be ran every time the structure under tree/ is updated.

images-thumbs.py

This script needs to be tweaked before it runs. It runs on a selection of directories, scanning for image files (png and jpg/jpeg). Upon discovery, it will generate large and small (thumnbail) .webp versions of the image, as well as a JPEG image - no png images are generated. These are needed due to efficiency concerns when loading many high-quality images at once - also .webp is a more modern format for web content.

requirements.txt

Lists the Python dependencies required to run the python scripts.

scripts/

Contains .js scripts used in the website.

header.js

Handles the dynamic generation of the header, including the search functionality, navigation links, and collapsable sidebar for taxonomy browsing.

language.js

Handles language selection and translation for the website.

journal.js

Handles language loading for journal pages.

navpath.js

Generates the navigation path (breadcrumbs) for the website based on the current page.

random-sample.js

Selects a random sample of species to display on the homepage. Relies on a static list of information for each sample and the available images. The list, together with the rest of the file are auto-generated. Any updates aimed for this file should be made in the template file (pyscripts/site_generator/templates/random-sample.js.template)

templates/

Contains header.html, used as a "template" to load the header in every page

tree/

Contains the hierarchical structure of the taxonomy, with one .html and one .json (translation metadata) file at each level.

index.html / index.json

The homepage. Manually maintained

map.html / map.json

A page that shows fossil locations on a map. Auto-generated.

server.py

A Python script to run a local server for testing the website.

style.css

Contains the CSS styles for the website.

unclassified.html / unclassified.json

Page that displays fossils that I wasn't able to assign to a taxon.