Gemini CLI Project Context: Academic Portfolio Website

This project is a personal academic and portfolio website built using Jekyll and the AcademicPages theme (a fork of Minimal Mistakes). It is designed to showcase publications, talks, teaching experience, and blog posts.

🚀 Purpose

To provide a structured, static website that hosts academic professional information, including:

• Publications: Research papers and articles.
• Talks: Presentations and tutorials.
• Teaching: Course information and materials.
• CV/Resume: Professional background.
• Blog: Personal or research-related updates.

🛠️ Technical Stack

• Static Site Generator: Jekyll (Ruby)
• Templating: Liquid
• Styling: SASS (compiled from _sass/)
• Scripting: Python & Jupyter Notebooks (for content generation)
• Deployment: Typically hosted via GitHub Pages.

📁 Key Project Structure

Content & Data

• _publications/: Markdown files for individual research papers.
• _talks/: Markdown files for presentations and tutorials.
• _teaching/: Markdown files for courses taught.
• _posts/: Markdown files for blog posts.
• _pages/: Static Markdown/HTML pages (e.g., about.md, cv.md, publications.md).
• _data/: Configuration data:
  • navigation.yml: Defines the main navigation menu.
  • authors.yml: Author profile information.
  • ui-text.yml: Localized UI strings.
• files/: PDFs of publications and other downloadable documents.
• images/: Profile pictures, logos, and images for posts/pages.

Layouts & Includes

• _layouts/: Page templates (e.g., single.html, talk.html, archive.html).
• _includes/: Reusable HTML fragments (e.g., head.html, footer.html, author-profile.html).

Styling & Assets

• _sass/: SCSS source files for the site’s design.
• assets/: Static assets including CSS, JavaScript, and fonts.

Content Generation

• markdown_generator/: Contains Python scripts (.py) and Jupyter notebooks (.ipynb) that automate the creation of Markdown files in _publications/ and _talks/ from bibliography files (.bib) or TSV data (.tsv).
• Conda Environment: A minimal conda environment academic-pages is used to run these scripts (requires pybtex and pandas).
  • Run scripts using: /Users/ymagen/miniconda3/envs/academic-pages/bin/python markdown_generator/pubsFromBib.py

⚙️ Configuration

• _config.yml: Central configuration file. Contains site title, author details, SEO settings, and collection definitions. This is the first place to look when modifying site-wide behavior.

📝 Workflow for LLM Agents

1. Adding a Publication/Talk

• Manual: Create a new Markdown file in _publications/ or _talks/ following the existing naming convention (e.g., YYYY-MM-DD-title-slug.md).
• Automated: Use scripts in markdown_generator/ if you have a BibTeX or TSV source.

2. Updating Navigation

• Modify _data/navigation.yml to add or remove links from the top menu.

3. Modifying the Author Profile

• Most author information is stored in _config.yml under the author key. Some themes might also use _data/authors.yml.

4. Running Locally

• Run bundle exec jekyll serve or bundle exec jekyll liveserve to preview changes locally.

5. Styling Changes

• Modify the corresponding SCSS file in _sass/. The entry point is assets/css/main.scss.

⚠️ Important Considerations

• Front Matter: Every page and collection item (post, publication, etc.) uses YAML front matter between --- markers. Ensure this is preserved and correctly formatted.
• Permalinks: Permalinks are often explicitly defined in the front matter to ensure stable URLs.
• Relative Paths: Use `` or the relative_url filter when linking to assets or other pages to ensure compatibility with different base URLs.