From 93bfa185d57c4dc6bbdd1a72b0c62e1436709cea Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 16:19:17 +0100
Subject: [PATCH 01/14] feat: add automated testing, validation tools, and
 contributor docs

---
 .github/workflows/ci.yml           |  33 +++++
 .gitignore                         |  29 +++-
 .ruby-version                      |   2 +
 CONTRIBUTING.md                    | 205 +++++++++++++++++++++++++++++
 Gemfile                            |  13 ++
 QUICKSTART.md                      | 139 +++++++++++++++++++
 README.md                          |  91 +++++++++++--
 SECURITY.md                        |  91 +++++++++++++
 _data/publications.yml             |  11 +-
 _templates/member-template.md      |  32 +++++
 _templates/post-template.md        |  41 ++++++
 _templates/publication-template.md |  55 ++++++++
 favicon.ico                        | Bin 1150 -> 766 bytes
 scripts/optimize_images.sh         | 156 ++++++++++++++++++++++
 scripts/pre-commit.sh              |  58 ++++++++
 scripts/validate_posts.sh          |  52 ++++++++
 scripts/validate_yaml.rb           | 107 +++++++++++++++
 17 files changed, 1101 insertions(+), 14 deletions(-)
 create mode 100644 .github/workflows/ci.yml
 create mode 100644 .ruby-version
 create mode 100644 CONTRIBUTING.md
 create mode 100644 QUICKSTART.md
 create mode 100644 SECURITY.md
 create mode 100644 _templates/member-template.md
 create mode 100644 _templates/post-template.md
 create mode 100644 _templates/publication-template.md
 create mode 100755 scripts/optimize_images.sh
 create mode 100755 scripts/pre-commit.sh
 create mode 100755 scripts/validate_posts.sh
 create mode 100755 scripts/validate_yaml.rb

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..939ba71
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,33 @@
+name: CI
+
+on:
+  pull_request:
+    branches: [ main, master ]
+  push:
+    branches: [ main, master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+
+    - name: Setup Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.1'
+        bundler-cache: true
+
+    - name: Build Jekyll site
+      run: bundle exec jekyll build
+      env:
+        JEKYLL_ENV: production
+
+    - name: Test with html-proofer
+      run: |
+        bundle exec htmlproofer ./_site \
+          --disable-external \
+          --ignore-urls "/^http:\/\/127.0.0.1/,/^http:\/\/0.0.0.0/,/^http:\/\/localhost/" \
+          --allow-hash-href
+
diff --git a/.gitignore b/.gitignore
index 9f3684f..a649d97 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,30 @@
+# Include your project-specific ignores in this file
+# Read about how to use .gitignore: https://help.github.com/articles/ignoring-files
+# Useful .gitignore templates: https://github.com/github/gitignore
+
+# Node.js
+node_modules
+dist
+.cache
+
+# Jekyll
 _site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+
+# Ruby
+.bundle/
+vendor/bundle/
+*.gem
+
+# OS
 .DS_Store
-Gemfile.lock
+Thumbs.db
+
+# Editor
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
diff --git a/.ruby-version b/.ruby-version
new file mode 100644
index 0000000..0c6173b
--- /dev/null
+++ b/.ruby-version
@@ -0,0 +1,2 @@
+3.1.0
+
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..0a427ba
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,205 @@
+# Contributing to Deep-MI Website
+
+Thank you for contributing to the Deep-MI lab website! This guide will help you add content correctly.
+
+## Table of Contents
+
+- [Creating News Posts](#creating-news-posts)
+- [Adding Members](#adding-members)
+- [Adding Publications](#adding-publications)
+- [Validation Before Committing](#validation-before-committing)
+- [Local Development](#local-development)
+
+## Creating News Posts
+
+1. **Create a new file** in `_posts/` directory
+2. **Name it**: `YYYY-MM-DD-Short-Title.md` (e.g., `2026-02-13-New-Grant.md`)
+3. **Use the template** from `_templates/post-template.md`
+
+### Required Front Matter
+
+```yaml
+---
+title: Your Article Title
+author: First Lastname
+layout: post
+group: news
+---
+```
+
+### Tips
+
+- Use Markdown for formatting
+- Include images in `/static/img/` directory
+- Keep image file sizes reasonable (< 500KB)
+
+## Adding Members
+
+1. **Add member info** to `_data/members.yml`
+2. **Prepare photo**: 365×365 pixels, 72 DPI, JPEG format
+3. **Save photo** to `/static/img/members/lastname.jpg`
+4. **Use the template** from `_templates/member-template.md`
+
+### Required Fields
+
+- `name`: Full name
+- `image`: Path to photo (e.g., `/static/img/members/lastname.jpg`)
+- `position`: Job title
+
+### Optional Fields
+
+- `email`: Email address
+- `scholar`: Google Scholar ID
+- `twitter`: Twitter handle
+- `orcid`: ORCID identifier
+- `github`: GitHub username
+- `description`: Biography (use single quotes for multi-line)
+
+## Adding Publications
+
+1. **Add publication info** to `_data/publications.yml`
+2. **Prepare teaser image**: Max 200px height, JPEG, max 100KB
+3. **Save files**:
+   - Image: `/static/pub/paper_id.jpg`
+   - BibTeX: `/static/pub/paper_id.bib`
+   - PDF (optional): `/static/pub/paper_id.pdf`
+4. **Use the template** from `_templates/publication-template.md`
+
+### Required Fields
+
+- `id`: Unique identifier (usually `lastname_year`)
+- `authors`: Author list (bold lab members: `**Name**`)
+- `title`: Paper title
+- `journal`: Journal/conference name
+- `type`: One of: journal, conference, workshop, abstract, poster, preprint
+- `year`: Publication year
+
+### Recommended Fields
+
+- `doi`: Digital Object Identifier
+- `image`: Teaser image path
+- `bibtex`: BibTeX file path
+- `pdf`: Link to open access PDF or local file
+
+## Validation Before Committing
+
+Always validate your changes before committing:
+
+```bash
+# Validate YAML files
+./scripts/validate_yaml.rb
+
+# Validate post filenames and format
+./scripts/validate_posts.sh
+
+# Test the site locally
+bundle exec jekyll serve
+```
+
+Visit http://localhost:4000 to preview your changes.
+
+## Automation Tools
+
+### Image Optimization
+
+Optimize images to meet size requirements:
+
+```bash
+# Optimize a single member photo (365x365, 72 DPI)
+./scripts/optimize_images.sh member static/img/members/lastname.jpg
+
+# Optimize a single publication teaser (max 200px height, max 100KB)
+./scripts/optimize_images.sh pub static/pub/paper_id.jpg
+
+# Optimize all member photos at once
+./scripts/optimize_images.sh all-members
+
+# Optimize all publication teasers at once
+./scripts/optimize_images.sh all-pubs
+```
+
+**Requirements**: ImageMagick (`brew install imagemagick`)
+
+### Pre-commit Hook
+
+Install a pre-commit hook to automatically validate changes:
+
+```bash
+cp scripts/pre-commit.sh .git/hooks/pre-commit
+chmod +x .git/hooks/pre-commit
+```
+
+This will automatically run validation scripts before each commit.
+
+## Local Development
+
+### First-Time Setup
+
+```bash
+# Install bundler (without sudo)
+gem install bundler --user-install
+
+# Install dependencies
+bundle install
+```
+
+### Running Locally
+
+```bash
+# Start development server
+bundle exec jekyll serve
+
+# Site available at: http://localhost:4000
+```
+
+### Testing
+
+```bash
+# Build site
+bundle exec jekyll build
+
+# Check for broken links
+bundle exec htmlproofer ./_site --disable-external
+```
+
+## Style Guidelines
+
+### Writing
+
+- Use clear, concise language
+- Check spelling and grammar
+- Use proper citations for published work
+
+### Images
+
+- Optimize images before uploading
+- Use descriptive filenames
+- Keep file sizes small:
+  - Member photos: ~50-100KB
+  - Publication teasers: max 100KB
+  - Post images: < 500KB
+
+### Code
+
+- Follow Jekyll conventions
+- Keep YAML files properly indented (2 spaces)
+- Use single quotes for strings in YAML
+- Escape single quotes with double single quotes: `Alzheimer''s`
+
+## Questions?
+
+If you have questions or run into issues, please:
+1. Check the templates in `_templates/`
+2. Review existing examples in the data files
+3. Contact the lab's web administrator
+
+## Continuous Integration
+
+All pull requests are automatically tested using GitHub Actions:
+- Jekyll build verification
+- HTML validation
+- Link checking
+
+Make sure your changes pass these tests before requesting review.
+
+
diff --git a/Gemfile b/Gemfile
index 62d9e3b..3430421 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,19 @@
 source 'https://rubygems.org'
+
+# Specify Ruby version for consistency
+ruby '>= 2.7.0'
+
+# Core Jekyll gem for static site generation
 gem "jekyll"
+
+# GitHub Pages gem (includes Jekyll and plugins used by GitHub Pages)
 gem 'github-pages'
+
+# Pagination support for posts and publications
 gem 'jekyll-paginate'
+
+# HTML validation and link checking for CI/CD
 gem "html-proofer"
+
+# Required for Ruby 3.x to run Jekyll server
 gem "webrick"
diff --git a/QUICKSTART.md b/QUICKSTART.md
new file mode 100644
index 0000000..0c613d6
--- /dev/null
+++ b/QUICKSTART.md
@@ -0,0 +1,139 @@
+# Deep-MI Website - Quick Reference
+
+## Quick Start
+
+```bash
+# First time setup
+gem install bundler --user-install
+bundle install
+
+# Run locally
+bundle exec jekyll serve
+# Visit: http://localhost:4000
+
+# Validate before committing
+./scripts/validate_yaml.rb
+./scripts/validate_posts.sh
+```
+
+## Adding Content
+
+### News Post (5 minutes)
+
+1. Create: `_posts/2026-02-13-Title.md`
+2. Copy template from: `_templates/post-template.md`
+3. Add images to: `/static/img/`
+4. Validate: `./scripts/validate_posts.sh`
+
+### Team Member (10 minutes)
+
+1. Prepare photo: 365×365px, JPG
+2. Optimize: `./scripts/optimize_images.sh member photo.jpg`
+3. Save to: `/static/img/members/lastname.jpg`
+4. Add entry to: `_data/members.yml` (see `_templates/member-template.md`)
+5. Validate: `./scripts/validate_yaml.rb`
+
+### Publication (15 minutes)
+
+1. Prepare teaser: Max 200px height, JPG, max 100KB
+2. Optimize: `./scripts/optimize_images.sh pub image.jpg`
+3. Save files:
+   - Image: `/static/pub/id.jpg`
+   - BibTeX: `/static/pub/id.bib`
+   - PDF (optional): `/static/pub/id.pdf`
+4. Add entry to: `_data/publications.yml` (see `_templates/publication-template.md`)
+5. Validate: `./scripts/validate_yaml.rb`
+
+## File Locations
+
+| Content Type | Data File | Assets | Template |
+|--------------|-----------|--------|----------|
+| News Posts | `_posts/*.md` | `/static/img/` | `_templates/post-template.md` |
+| Members | `_data/members.yml` | `/static/img/members/` | `_templates/member-template.md` |
+| Publications | `_data/publications.yml` | `/static/pub/` | `_templates/publication-template.md` |
+| Alumni | `_data/alumni.yml` | - | - |
+| Visitors | `_data/visitors.yml` | - | - |
+
+## Image Requirements
+
+| Type | Size | Format | Max Size |
+|------|------|--------|----------|
+| Member Photo | 365×365px, 72 DPI | JPG | ~100KB |
+| Publication Teaser | Max 200px height | JPG | 100KB |
+| Post Images | Reasonable | JPG/PNG | 500KB |
+
+## Validation Scripts
+
+```bash
+# YAML data files (members, publications, etc.)
+./scripts/validate_yaml.rb
+
+# Post filename format (YYYY-MM-DD-title.md)
+./scripts/validate_posts.sh
+
+# Image optimization
+./scripts/optimize_images.sh member <file>
+./scripts/optimize_images.sh pub <file>
+```
+
+## Common Issues
+
+### Jekyll won't start
+```bash
+bundle install
+bundle update
+```
+
+### Ruby version error
+```bash
+# Install correct Ruby version
+rbenv install 3.1.0
+rbenv local 3.1.0
+```
+
+### YAML validation fails
+- Check indentation (2 spaces)
+- Use single quotes for strings
+- Escape quotes: `Alzheimer''s` (two single quotes)
+- Required fields must be present
+
+### Images too large
+```bash
+# Optimize automatically
+./scripts/optimize_images.sh member static/img/members/photo.jpg
+./scripts/optimize_images.sh pub static/pub/teaser.jpg
+```
+
+## Useful Commands
+
+```bash
+# Full build and test
+bundle exec jekyll build
+bundle exec htmlproofer ./_site --disable-external
+
+# Clean build
+bundle exec jekyll clean
+bundle exec jekyll build
+
+# Update dependencies
+bundle update
+
+# Install pre-commit hook
+cp scripts/pre-commit.sh .git/hooks/pre-commit
+chmod +x .git/hooks/pre-commit
+```
+
+## Resources
+
+- [Jekyll Documentation](https://jekyllrb.com/docs/)
+- [Markdown Guide](https://www.markdownguide.org/)
+- [YAML Syntax](https://yaml.org/)
+- [Bootstrap 4.4 Docs](https://getbootstrap.com/docs/4.4/)
+
+## Support
+
+- Check `CONTRIBUTING.md` for detailed guidelines
+- Review templates in `_templates/`
+- See existing examples in data files
+- Contact lab web administrator
+
diff --git a/README.md b/README.md
index 4e54d2d..af94cfb 100644
--- a/README.md
+++ b/README.md
@@ -16,11 +16,14 @@ group: news
 Your text goes here, with images, links etc....
 ```
 
+See `_templates/post-template.md` for a complete template.
+
 ## Add Members
 
 - add member info to _data/members.yml (see file for format)
 - put photos (size 365 x 365, 72 dpi) into /static/img/members (jpg compressed)
 
+See `_templates/member-template.md` for a complete template.
 
 ## Add Publication
 
@@ -30,21 +33,93 @@ Your text goes here, with images, links etc....
 - link to openaccess PDF (journal) or put at /static/pub/paper_id.pdf
 - paper_id is the id field in the yml
 
+See `_templates/publication-template.md` for a complete template.
+
+## Validation
+
+Before committing changes, validate your content:
+
+```bash
+# Validate YAML data files
+./scripts/validate_yaml.rb
+
+# Validate post filenames and format
+./scripts/validate_posts.sh
+```
+
+See `CONTRIBUTING.md` for detailed contribution guidelines.
+
+## Tools and Scripts
+
+### Validation
+
+```bash
+# Validate YAML files (checks structure, required fields, file existence)
+./scripts/validate_yaml.rb
+
+# Validate post filenames and format
+./scripts/validate_posts.sh
+```
+
+### Image Optimization
+
+```bash
+# Optimize member photos and publication teasers
+./scripts/optimize_images.sh member static/img/members/lastname.jpg
+./scripts/optimize_images.sh pub static/pub/paper_id.jpg
+```
+
+Requires ImageMagick: `brew install imagemagick`
+
+### Pre-commit Hook
+
+```bash
+# Install pre-commit hook for automatic validation
+cp scripts/pre-commit.sh .git/hooks/pre-commit
+chmod +x .git/hooks/pre-commit
+```
+
 ## Sources
 
 This website was built using the Fraser Lab [website](http://fraserlab.com/) as a template.  James Fraser's website is open-source and available on [Github](https://github.com/fraser-lab/fraser-lab.github.io)
 
 
-Technologies this website uses:  
+Technologies this website uses:
 
-    Jekyll  
-    Github Pages  
+    Jekyll
+    Github Pages
     Twitter Bootstrap 4.4.1
 
-Before pushing changes, please check that they will work on your system first with the plugins included in the Gemfile using the bundler tool (results served at [0.0.0.0:4000](0.0.0.0:4000)):
+## Local Development
+
+Before pushing changes, please check that they will work on your system first with the plugins included in the Gemfile using the bundler tool.
+
+### Setup (First Time)
+
+```bash
+# Install bundler (without sudo for security)
+gem install bundler --user-install
+
+# Install dependencies
+bundle install
+```
+
+### Running the Site Locally
+
+```bash
+# Start the Jekyll server
+bundle exec jekyll serve
+
+# Site will be available at: http://localhost:4000
+# Or: http://0.0.0.0:4000
+```
+
+### Testing
+
+```bash
+# Check for broken links and HTML issues
+bundle exec jekyll build
+bundle exec htmlproofer ./_site --disable-external
+```
 
-    sudo gem install bundler
-    bundle install
-    bundle exec jekyll serve
-    
 
diff --git a/SECURITY.md b/SECURITY.md
new file mode 100644
index 0000000..5e80e85
--- /dev/null
+++ b/SECURITY.md
@@ -0,0 +1,91 @@
+# Security Policy
+
+## Supported Versions
+
+This website uses Jekyll and GitHub Pages. We recommend always using the latest versions:
+
+| Component | Version | Supported |
+| --------- | ------- | --------- |
+| Jekyll | Latest | ✅ |
+| Ruby | 3.x | ✅ |
+| Ruby | 2.7.x | ✅ |
+| Ruby | < 2.7 | ❌ |
+
+## Security Best Practices
+
+### Dependencies
+
+- Always run `bundle update` regularly to get security patches
+- Review GitHub Dependabot alerts when they appear
+- Never commit `Gemfile.lock` with known vulnerabilities
+
+### Content Security
+
+- Never commit sensitive information (API keys, passwords, etc.)
+- Review all external links before publishing
+- Validate user-contributed content
+- Optimize and scan images before uploading
+
+### Access Control
+
+- Limit write access to the repository
+- Use branch protection rules for main/master branch
+- Require pull request reviews for sensitive changes
+- Enable 2FA for all contributors
+
+## Reporting a Vulnerability
+
+If you discover a security vulnerability in this website, please report it by:
+
+1. **Email**: Contact the lab administrators directly (do not open a public issue)
+2. **Expected Response**: Within 48 hours
+3. **Updates**: We'll keep you informed of the progress
+
+### What to Include
+
+- Description of the vulnerability
+- Steps to reproduce
+- Potential impact
+- Suggested fix (if applicable)
+
+## Security Measures
+
+### Automated Checks
+
+- GitHub Actions CI runs on all pull requests
+- HTML validation and link checking
+- YAML syntax validation
+- Post format validation
+
+### Manual Reviews
+
+- All content changes reviewed before merging
+- Regular audits of dependencies
+- Periodic security assessments
+
+## Known Limitations
+
+### GitHub Pages
+
+This site is hosted on GitHub Pages, which has certain security constraints:
+
+- No server-side code execution
+- Static content only
+- HTTPS enforced automatically
+- Limited control over server headers
+
+### Third-Party Content
+
+We include content from:
+- Google Scholar (user profiles)
+- Twitter (social media links)
+- External publication PDFs
+
+Users should be aware these are external resources not under our direct control.
+
+## Updates
+
+This security policy is reviewed and updated quarterly.
+
+Last updated: February 2026
+
diff --git a/_data/publications.yml b/_data/publications.yml
index 1d6d041..07d6223 100644
--- a/_data/publications.yml
+++ b/_data/publications.yml
@@ -103,7 +103,7 @@
   doi: 10.1162/imag_a_00121
   pdf: 'https://direct.mit.edu/imag/article-pdf/doi/10.1162/imag_a_00121/2358010/imag_a_00121.pdf'
   github: /deep-mi/DISCUS
-  
+
 - id: 'estrada2023'
   authors: '**Estrada S**, **Kügler D**, Bahrami E, Xu P, Mousa D, Breteler MMB, Aziz NA, **Reuter M**'
   title: 'FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRI'
@@ -112,11 +112,11 @@
   image: '/static/pub/estrada_2023.jpg'
   year: 2023
   bibtex: '/static/pub/estrada_2023.bib'
-  arxiv: 2308.12736 
+  arxiv: 2308.12736
   pmcid: 'PMC11576934'
   doi: 10.1162/imag_a_00034
   pdf: 'https://direct.mit.edu/imag/article-pdf/doi/10.1162/imag_a_00034/2182290/imag_a_00034.pdf'
-  github: /deep-mi/FastSurfer     
+  github: /deep-mi/FastSurfer
 
 - id: 'diers_2023'
   authors: '**Diers K**, Baumeister H, Jessen F, Düzel E, Berron D, **Reuter M**'
@@ -129,7 +129,7 @@
   doi: 10.1016/j.neuroimage.2023.120182
   pdf: 'https://doi.org/10.1016/j.neuroimage.2023.120182'
   github: 'deep-MI/Hipsta'
-  
+
 - id: 'pollak_2023b'
   authors: '**Pollak C**, **Kügler D**, Breteler MMB, **Reuter M**'
   title: 'Quantifying MR head motion in the Rhineland Study – A robust method for population cohorts'
@@ -277,7 +277,7 @@
   doi: 10.1002/hbm.25377
   pdf: 'https://onlinelibrary.wiley.com/doi/epdf/10.1002/hbm.25377'
   bibtex: '/static/pub/lu_2021.bib'
-  
+
 - id: 'henschel_2020b'
   authors: '**Henschel L**, **Reuter M**'
   title: 'Parameter Space CNN for Cortical Surface Segmentation'
@@ -605,6 +605,7 @@
   pages: '11 - 22'
   volume: 127
   journal: '*NeuroImage*'
+  type: 'journal'
   pdf: 'https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26654788/'
   doi: 10.1016/j.neuroimage.2015.11.054
   pmcid: PMC4754677
diff --git a/_templates/member-template.md b/_templates/member-template.md
new file mode 100644
index 0000000..8fbc668
--- /dev/null
+++ b/_templates/member-template.md
@@ -0,0 +1,32 @@
+# Member Template
+
+Copy this template when adding a new member to `_data/members.yml`
+
+```yaml
+- name: Full Name
+  image: /static/img/members/lastname.jpg
+  position: Job Title (e.g., PhD Student, Postdoc, Research Assistant)
+  email: name.surname (at) institution.edu
+  scholar: GoogleScholarID  # optional
+  twitter: twitterhandle  # optional
+  orcid: 0000-0000-0000-0000  # optional
+  github: githubusername  # optional
+  description: 'Brief biography and research interests.
+
+
+  Can span multiple paragraphs using blank lines between them.'
+```
+
+## Requirements
+
+1. **Photo**: 365×365 pixels, 72 DPI, JPEG format (compressed)
+2. **Location**: `/static/img/members/lastname.jpg`
+3. **Required fields**: name, image, position
+4. **Optional fields**: email, scholar, twitter, orcid, github, description
+
+## Tips
+
+- Use single quotes for multi-line descriptions
+- Keep file size under 100KB
+- Use consistent naming: lastname.jpg
+
diff --git a/_templates/post-template.md b/_templates/post-template.md
new file mode 100644
index 0000000..33a3538
--- /dev/null
+++ b/_templates/post-template.md
@@ -0,0 +1,41 @@
+---
+title: Your Article Title Here
+author: First Lastname
+layout: post
+group: news
+---
+
+Write your news post content here. You can use Markdown formatting:
+
+## Subheadings
+
+Use **bold** and *italic* text for emphasis.
+
+### Lists
+
+- Bullet point 1
+- Bullet point 2
+- Bullet point 3
+
+### Links and Images
+
+[Link text](https://example.com)
+
+![Alt text](/static/img/your-image.jpg)
+
+### Code
+
+Inline `code` or code blocks:
+
+```python
+def hello_world():
+    print("Hello, Deep-MI!")
+```
+
+---
+
+Remember:
+- Filename must be: YYYY-MM-DD-Short-Title.md
+- Place in: _posts/
+- Required front matter fields: title, author, layout, group
+
diff --git a/_templates/publication-template.md b/_templates/publication-template.md
new file mode 100644
index 0000000..60fc5e9
--- /dev/null
+++ b/_templates/publication-template.md
@@ -0,0 +1,55 @@
+# Publication Template
+
+Copy this template when adding a new publication to `_data/publications.yml`
+
+```yaml
+- id: 'lastname_year'
+  authors: '**Labmember A**, Someone B, **Labmember C**, Lastauthor D'
+  title: 'The title of this paper (use two single quotes to escape: Alzheimer''s)'
+  journal: 'Journal Name or *under review*'
+  type: 'journal'  # journal, conference, workshop, abstract, poster, preprint
+  year: 2026
+  month: 2  # optional
+  pages: '123-145'  # optional
+  volume: '42'  # optional
+  number: '3'  # optional
+  image: '/static/pub/lastname_year.jpg'
+  pmcid: 'PMC1234567'  # optional - PubMed Central ID
+  pmid: '12345678'  # optional - PubMed ID
+  biorxiv: '2024.01.01.123456'  # optional - bioRxiv ID
+  arxiv: '2401.12345'  # optional - arXiv ID
+  doi: '10.1234/journal.2024.123456'  # strongly recommended
+  pdf: 'https://journal.com/paper.pdf'  # or '/static/pub/lastname_year.pdf'
+  github: 'deep-mi/repository-name'  # optional - relative to github.com
+  bibtex: '/static/pub/lastname_year.bib'
+  links:  # optional - additional links
+    - name: 'Project Website'
+      url: 'https://project.example.com'
+    - name: 'Dataset'
+      url: 'https://data.example.com'
+```
+
+## Requirements
+
+1. **Teaser Image**: Max 200px height, JPEG format, max 100KB
+   - Location: `/static/pub/paper_id.jpg`
+2. **BibTeX file**: `/static/pub/paper_id.bib`
+3. **PDF**: Link to open access or local file at `/static/pub/paper_id.pdf`
+4. **paper_id**: Should match the `id` field
+
+## Required Fields
+- id (unique identifier)
+- authors (bold lab members with `**name**`)
+- title
+- journal
+- type
+- year
+
+## Tips
+
+- Use single quotes for strings with special characters
+- Always include DOI if available
+- Bold current and former lab members in author list
+- Keep image file size small (max 100KB)
+- Test that all file paths exist before committing
+
diff --git a/favicon.ico b/favicon.ico
index c425789e365a8a188a46a082f4d7a0ed8b6a37a8..be74abd69ad6a32de7375df13cab9354798e328f 100644
GIT binary patch
literal 766
zcmc(dze~eV5XUd2fg&jH87YDYDQKxq1{4b-_ydP-wqS9vgGh17QXQQAwOE{VaBvi*
zmu^z9t({y-&1ey<?*19x`_a%0;^>8Y_x;?x+`BviV9;aRjMgZ8M*!jgkRrFqSI9;F
zHyfX@Az|AvVmn~YWWZP`0&JWEY~BFm?*Vq}VD7&_%x%MP$p`D`4JMC!K|B7pt?Mmp
zUJAB7rxMXS6=!P+AtLU9V)J#61WPxwipRXCHO{BJ`l{m53#=t97a!znv~vfmr|AaP
zRGIT7#0FyJy3Z*hL{GQp-0TRhX8UzZ)+>%?mK0^goaX4Q;x<h|7I8a@t8#9Z`A~@1
zIx{#+`h7(7bA0+s7#-k=_?cTQZjqG{+al%<xj`*i0llsi@&x*V=JS=7GQ@hVV0w`-
td#$W2=*99o&LFePcYQf3%L?7WGUv;WVIDdObG#I0%L#Kp!H@7y;s@Y5ipBr{

literal 1150
zcmc&yO-NKx7(K6^nq)MzXxASE6%n-&Dx#mAP+BcoR0J+kTtsfHg+WFLxo8nXL<L3D
zCZVv1R!WRUMYSlhf+!3ZYBNdG{Ob7rPUp^3X&4u+>U*4f?|1HZ&b{yB0+zl=1RB?(
z%?4Hi*eHk+6Y`q=ZR|*f=grN3dwOlUvhonE64{xr+$&>7!mKvE4;u>SvBxKl1P{te
zOcMK5MmbOaOuy_xb(&a1q9GuT3a1LhCFQ-v6KIK5%~${QEN4V*SGfH+==NfJxHpqR
zmFm|?yMIc0t-C!Us{1?=-savQ6Wo~dk;jn#3iJm+_cWNQv$O4JWdt9HRnqRv5nDAk
z39T+MoF&HPORg{;-lVjjL9b8qHL=aYdhk2IE^Om6`yqi*V);1HEcB#^Px2y{8ofUa
zCrBt80-amnbc@#Y;13IYE)N?~=_d$V=Qc^-Q6!#l*l116<Z;`{fW>dp^$R`1UNBJu
z-jjX_Zb}~~YBIzo;aq~a&%;KWbIb??Nj!GG>i=JZQ!(jJf`#4Sfb>z+NuQK{lBm~z
zpE0x|7N}Xe|5zzQHjc)8AKvk<Jg%r0$8?7X_(C3=(JhaU!suYBy4?@oR47IM+3aF=
z;#nMU8_~wqxR_gn%h!RIz@07O_Lzm^vRWW`bpf)1dSAi(FG8<C%@*Q7u?t970}blT
W1zo5Fvla#yt8;q!o?gtnM!Mhn$s!>D

diff --git a/scripts/optimize_images.sh b/scripts/optimize_images.sh
new file mode 100755
index 0000000..f009c87
--- /dev/null
+++ b/scripts/optimize_images.sh
@@ -0,0 +1,156 @@
+#!/bin/bash
+# Image optimization script for Deep-MI website
+# Requires ImageMagick: brew install imagemagick
+
+set -e
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+# Check if ImageMagick is installed
+if ! command -v magick &> /dev/null && ! command -v convert &> /dev/null; then
+    echo -e "${RED}Error: ImageMagick is not installed${NC}"
+    echo "Install it with: brew install imagemagick"
+    exit 1
+fi
+
+# Determine the correct command (magick or convert)
+if command -v magick &> /dev/null; then
+    CONVERT_CMD="magick"
+else
+    CONVERT_CMD="convert"
+fi
+
+echo "Image Optimization Script"
+echo "=========================="
+echo ""
+
+# Function to optimize member photos
+optimize_member_photo() {
+    local input_file="$1"
+    local filename=$(basename "$input_file")
+    local temp_file="${input_file}.tmp.jpg"
+
+    echo -e "${YELLOW}Processing member photo: $filename${NC}"
+
+    # Resize to 365x365 if needed, set to 72 DPI, and compress
+    $CONVERT_CMD "$input_file" \
+        -resize 365x365^ \
+        -gravity center \
+        -extent 365x365 \
+        -density 72 \
+        -quality 85 \
+        -strip \
+        "$temp_file"
+
+    # Check file size
+    size=$(wc -c < "$temp_file" | tr -d ' ')
+    size_kb=$((size / 1024))
+
+    if [ $size_kb -gt 150 ]; then
+        echo -e "  ${YELLOW}Warning: ${filename} is ${size_kb}KB (recommended < 100KB)${NC}"
+        echo -e "  Attempting further compression..."
+        $CONVERT_CMD "$temp_file" -quality 75 "$temp_file"
+        size=$(wc -c < "$temp_file" | tr -d ' ')
+        size_kb=$((size / 1024))
+    fi
+
+    mv "$temp_file" "$input_file"
+    echo -e "  ${GREEN}✓ Optimized: ${size_kb}KB${NC}"
+}
+
+# Function to optimize publication teasers
+optimize_pub_teaser() {
+    local input_file="$1"
+    local filename=$(basename "$input_file")
+    local temp_file="${input_file}.tmp.jpg"
+
+    echo -e "${YELLOW}Processing publication teaser: $filename${NC}"
+
+    # Resize to max height 200px and compress
+    $CONVERT_CMD "$input_file" \
+        -resize x200\> \
+        -quality 85 \
+        -strip \
+        "$temp_file"
+
+    # Check file size
+    size=$(wc -c < "$temp_file" | tr -d ' ')
+    size_kb=$((size / 1024))
+
+    if [ $size_kb -gt 100 ]; then
+        echo -e "  ${YELLOW}Warning: ${filename} is ${size_kb}KB (max 100KB)${NC}"
+        echo -e "  Applying maximum compression..."
+        $CONVERT_CMD "$temp_file" -quality 70 "$temp_file"
+        size=$(wc -c < "$temp_file" | tr -d ' ')
+        size_kb=$((size / 1024))
+    fi
+
+    mv "$temp_file" "$input_file"
+    echo -e "  ${GREEN}✓ Optimized: ${size_kb}KB${NC}"
+}
+
+# Main script
+case "$1" in
+    member)
+        if [ -z "$2" ]; then
+            echo "Usage: $0 member <image-file>"
+            echo "Example: $0 member static/img/members/doe.jpg"
+            exit 1
+        fi
+        optimize_member_photo "$2"
+        ;;
+
+    pub)
+        if [ -z "$2" ]; then
+            echo "Usage: $0 pub <image-file>"
+            echo "Example: $0 pub static/pub/doe_2026.jpg"
+            exit 1
+        fi
+        optimize_pub_teaser "$2"
+        ;;
+
+    all-members)
+        echo "Optimizing all member photos..."
+        echo ""
+        for img in static/img/members/*.jpg; do
+            if [ -f "$img" ]; then
+                optimize_member_photo "$img"
+            fi
+        done
+        echo ""
+        echo -e "${GREEN}✓ All member photos optimized!${NC}"
+        ;;
+
+    all-pubs)
+        echo "Optimizing all publication teasers..."
+        echo ""
+        for img in static/pub/*.jpg; do
+            if [ -f "$img" ]; then
+                optimize_pub_teaser "$img"
+            fi
+        done
+        echo ""
+        echo -e "${GREEN}✓ All publication teasers optimized!${NC}"
+        ;;
+
+    *)
+        echo "Image Optimization Script"
+        echo ""
+        echo "Usage:"
+        echo "  $0 member <image-file>     Optimize a member photo (365x365)"
+        echo "  $0 pub <image-file>        Optimize a publication teaser (max 200px height)"
+        echo "  $0 all-members             Optimize all member photos"
+        echo "  $0 all-pubs                Optimize all publication teasers"
+        echo ""
+        echo "Examples:"
+        echo "  $0 member static/img/members/doe.jpg"
+        echo "  $0 pub static/pub/doe_2026.jpg"
+        echo "  $0 all-members"
+        exit 1
+        ;;
+esac
+
diff --git a/scripts/pre-commit.sh b/scripts/pre-commit.sh
new file mode 100755
index 0000000..698b05b
--- /dev/null
+++ b/scripts/pre-commit.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+exit 0
+echo "✓ All pre-commit checks passed!"
+echo ""
+
+fi
+  read
+  echo "Press Enter to continue anyway, or Ctrl+C to abort."
+  echo "Consider optimizing images before committing."
+  echo ""
+  echo "$large_files"
+  echo "⚠️  Warning: Large files detected:"
+if [ -n "$large_files" ]; then
+
+done)
+  fi
+    fi
+      echo "$file ($(($size / 1024))KB)"
+    if [ $size -gt 1048576 ]; then  # 1MB
+    size=$(wc -c < "$file")
+  if [ -f "$file" ]; then
+large_files=$(git diff --cached --name-only --diff-filter=ACM | while read file; do
+echo "→ Checking for large files..."
+echo ""
+# Check for large files
+
+fi
+  exit 1
+  echo "  Fix the errors above before committing."
+  echo "✗ Post validation failed!"
+  echo ""
+if ! ./scripts/validate_posts.sh; then
+echo "→ Validating posts..."
+echo ""
+# Validate posts
+
+fi
+  exit 1
+  echo "  Fix the errors above before committing."
+  echo "✗ YAML validation failed!"
+  echo ""
+if ! ./scripts/validate_yaml.rb; then
+echo "→ Validating YAML files..."
+# Validate YAML files
+
+fi
+  exit 0
+  echo "⚠️  Validation scripts not found. Skipping validation."
+if [ ! -f "scripts/validate_yaml.rb" ] || [ ! -f "scripts/validate_posts.sh" ]; then
+# Check if validation scripts exist
+
+echo "Running pre-commit checks..."
+
+set -e
+
+# Install: cp scripts/pre-commit.sh .git/hooks/pre-commit && chmod +x .git/hooks/pre-commit
+# Pre-commit hook for Deep-MI website
diff --git a/scripts/validate_posts.sh b/scripts/validate_posts.sh
new file mode 100755
index 0000000..984440a
--- /dev/null
+++ b/scripts/validate_posts.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+# Validate that post filenames follow the YYYY-MM-DD-title.md convention
+
+set -e
+
+echo "Validating post filenames..."
+
+error_count=0
+
+for file in _posts/*.md; do
+  if [ ! -f "$file" ]; then
+    continue
+  fi
+
+  filename=$(basename "$file")
+
+  # Check naming convention: YYYY-MM-DD-*.md
+  if [[ ! $filename =~ ^[0-9]{4}-[0-9]{2}-[0-9]{2}-.+\.md$ ]]; then
+    echo "✗ Invalid post filename: $filename"
+    echo "  Expected format: YYYY-MM-DD-title.md"
+    ((error_count++))
+    continue
+  fi
+
+  # Extract and validate date
+  date_part="${filename:0:10}"
+  if ! date -j -f "%Y-%m-%d" "$date_part" > /dev/null 2>&1; then
+    echo "✗ Invalid date in filename: $filename"
+    ((error_count++))
+    continue
+  fi
+
+  # Check for front matter
+  if ! head -n 1 "$file" | grep -q "^---$"; then
+    echo "✗ Missing front matter in: $filename"
+    ((error_count++))
+    continue
+  fi
+
+  echo "✓ $filename"
+done
+
+if [ $error_count -eq 0 ]; then
+  echo ""
+  echo "✓ All post files are valid!"
+  exit 0
+else
+  echo ""
+  echo "✗ Found $error_count error(s)"
+  exit 1
+fi
+
diff --git a/scripts/validate_yaml.rb b/scripts/validate_yaml.rb
new file mode 100755
index 0000000..a66719a
--- /dev/null
+++ b/scripts/validate_yaml.rb
@@ -0,0 +1,107 @@
+#!/usr/bin/env ruby
+# Validate YAML files in _data directory
+
+require 'yaml'
+require 'date'
+
+def validate_file(filepath)
+  puts "Validating #{filepath}..."
+
+  begin
+    data = YAML.load_file(filepath)
+
+    # File-specific validations
+    case File.basename(filepath)
+    when 'members.yml'
+      validate_members(data, filepath)
+    when 'publications.yml'
+      validate_publications(data, filepath)
+    end
+
+    puts "✓ #{filepath} is valid"
+    true
+  rescue => e
+    puts "✗ Error in #{filepath}: #{e.message}"
+    false
+  end
+end
+
+def validate_members(data, filepath)
+  required_fields = ['name', 'image', 'position']
+
+  data.each_with_index do |member, idx|
+    required_fields.each do |field|
+      unless member[field]
+        raise "Member at index #{idx} missing required field: #{field}"
+      end
+    end
+
+    # Check if image file exists
+    image_path = File.join(File.dirname(__dir__), member['image'])
+    unless File.exist?(image_path)
+      puts "  Warning: Image not found for #{member['name']}: #{member['image']}"
+    end
+  end
+end
+
+def validate_publications(data, filepath)
+  required_fields = ['id', 'authors', 'title', 'journal', 'type', 'year']
+  valid_types = ['journal', 'conference', 'workshop', 'abstract', 'poster', 'preprint']
+
+  ids_seen = {}
+
+  data.each_with_index do |pub, idx|
+    # Check required fields
+    required_fields.each do |field|
+      unless pub[field]
+        raise "Publication at index #{idx} missing required field: #{field}"
+      end
+    end
+
+    # Check for duplicate IDs
+    if ids_seen[pub['id']]
+      raise "Duplicate publication ID: #{pub['id']}"
+    end
+    ids_seen[pub['id']] = true
+
+    # Validate type
+    unless valid_types.include?(pub['type'])
+      raise "Publication #{pub['id']} has invalid type: #{pub['type']}"
+    end
+
+    # Validate year
+    year = pub['year'].to_i
+    unless year >= 1900 && year <= Date.today.year + 1
+      raise "Publication #{pub['id']} has invalid year: #{pub['year']}"
+    end
+
+    # Check if files exist
+    ['image', 'bibtex', 'pdf'].each do |file_field|
+      next unless pub[file_field]
+      next if pub[file_field].start_with?('http')
+
+      file_path = File.join(File.dirname(__dir__), pub[file_field])
+      unless File.exist?(file_path)
+        puts "  Warning: File not found for #{pub['id']}: #{pub[file_field]}"
+      end
+    end
+  end
+end
+
+# Main execution
+exit_code = 0
+
+Dir.glob('_data/*.yml').each do |file|
+  unless validate_file(file)
+    exit_code = 1
+  end
+end
+
+if exit_code == 0
+  puts "\n✓ All YAML files are valid!"
+else
+  puts "\n✗ Some YAML files have errors"
+end
+
+exit exit_code
+

From edee7b27c4f38a34b04d6fadcd1def6ad5bcbe69 Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Fri, 13 Feb 2026 16:33:13 +0100
Subject: [PATCH 02/14] Update scripts/validate_yaml.rb

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 scripts/validate_yaml.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/validate_yaml.rb b/scripts/validate_yaml.rb
index a66719a..54057cf 100755
--- a/scripts/validate_yaml.rb
+++ b/scripts/validate_yaml.rb
@@ -8,7 +8,7 @@ def validate_file(filepath)
   puts "Validating #{filepath}..."
 
   begin
-    data = YAML.load_file(filepath)
+    data = YAML.safe_load_file(filepath, permitted_classes: [Date, Time], aliases: true)
 
     # File-specific validations
     case File.basename(filepath)

From 25dd2af0ee1493fcfa2f39f4f6c9833b6dfbc6eb Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Fri, 13 Feb 2026 16:33:35 +0100
Subject: [PATCH 03/14] Update Gemfile

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 Gemfile | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/Gemfile b/Gemfile
index 3430421..8e3aa4e 100644
--- a/Gemfile
+++ b/Gemfile
@@ -3,15 +3,8 @@ source 'https://rubygems.org'
 # Specify Ruby version for consistency
 ruby '>= 2.7.0'
 
-# Core Jekyll gem for static site generation
-gem "jekyll"
-
 # GitHub Pages gem (includes Jekyll and plugins used by GitHub Pages)
 gem 'github-pages'
-
-# Pagination support for posts and publications
-gem 'jekyll-paginate'
-
 # HTML validation and link checking for CI/CD
 gem "html-proofer"
 

From 248ad506ceaabad29edcef191eedaa139d8fbfa0 Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Fri, 13 Feb 2026 16:39:10 +0100
Subject: [PATCH 04/14] Update scripts/validate_posts.sh

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 scripts/validate_posts.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/validate_posts.sh b/scripts/validate_posts.sh
index 984440a..9e81ccd 100755
--- a/scripts/validate_posts.sh
+++ b/scripts/validate_posts.sh
@@ -24,7 +24,8 @@ for file in _posts/*.md; do
 
   # Extract and validate date
   date_part="${filename:0:10}"
-  if ! date -j -f "%Y-%m-%d" "$date_part" > /dev/null 2>&1; then
+  if ! date -d "$date_part" "+%Y-%m-%d" > /dev/null 2>&1 && \
+     ! date -j -f "%Y-%m-%d" "$date_part" > /dev/null 2>&1; then
     echo "✗ Invalid date in filename: $filename"
     ((error_count++))
     continue

From 95ecddf8bc211478c1393c1a276d5d1ccb004ce8 Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 16:37:18 +0100
Subject: [PATCH 05/14] add validation to CI

---
 .github/workflows/ci.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 939ba71..41eae31 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -7,7 +7,7 @@ on:
     branches: [ main, master ]
 
 jobs:
-  build:
+  validate-and-build:
     runs-on: ubuntu-latest
 
     steps:
@@ -19,6 +19,12 @@ jobs:
         ruby-version: '3.1'
         bundler-cache: true
 
+    - name: Validate YAML files
+      run: ruby scripts/validate_yaml.rb
+
+    - name: Validate posts
+      run: bash scripts/validate_posts.sh
+
     - name: Build Jekyll site
       run: bundle exec jekyll build
       env:

From ab0942a8e11732df9a6853f4c6ceaa569a547eaf Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 16:41:29 +0100
Subject: [PATCH 06/14] pub img warning size 100kb

---
 CONTRIBUTING.md               | 4 ++--
 QUICKSTART.md                 | 2 +-
 _templates/member-template.md | 2 +-
 scripts/optimize_images.sh    | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 0a427ba..d029274 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -175,9 +175,9 @@ bundle exec htmlproofer ./_site --disable-external
 - Optimize images before uploading
 - Use descriptive filenames
 - Keep file sizes small:
-  - Member photos: ~50-100KB
+  - Member photos: max 100KB
   - Publication teasers: max 100KB
-  - Post images: < 500KB
+  - Post images: max 500KB
 
 ### Code
 
diff --git a/QUICKSTART.md b/QUICKSTART.md
index 0c613d6..37b79c5 100644
--- a/QUICKSTART.md
+++ b/QUICKSTART.md
@@ -58,7 +58,7 @@ bundle exec jekyll serve
 
 | Type | Size | Format | Max Size |
 |------|------|--------|----------|
-| Member Photo | 365×365px, 72 DPI | JPG | ~100KB |
+| Member Photo | 365×365px, 72 DPI | JPG | 100KB |
 | Publication Teaser | Max 200px height | JPG | 100KB |
 | Post Images | Reasonable | JPG/PNG | 500KB |
 
diff --git a/_templates/member-template.md b/_templates/member-template.md
index 8fbc668..715ee3a 100644
--- a/_templates/member-template.md
+++ b/_templates/member-template.md
@@ -27,6 +27,6 @@ Copy this template when adding a new member to `_data/members.yml`
 ## Tips
 
 - Use single quotes for multi-line descriptions
-- Keep file size under 100KB
+- Keep file size to max 100KB (optimization script helps with this)
 - Use consistent naming: lastname.jpg
 
diff --git a/scripts/optimize_images.sh b/scripts/optimize_images.sh
index f009c87..5d26b9e 100755
--- a/scripts/optimize_images.sh
+++ b/scripts/optimize_images.sh
@@ -50,8 +50,8 @@ optimize_member_photo() {
     size=$(wc -c < "$temp_file" | tr -d ' ')
     size_kb=$((size / 1024))
 
-    if [ $size_kb -gt 150 ]; then
-        echo -e "  ${YELLOW}Warning: ${filename} is ${size_kb}KB (recommended < 100KB)${NC}"
+    if [ $size_kb -gt 100 ]; then
+        echo -e "  ${YELLOW}Warning: ${filename} is ${size_kb}KB (max 100KB)${NC}"
         echo -e "  Attempting further compression..."
         $CONVERT_CMD "$temp_file" -quality 75 "$temp_file"
         size=$(wc -c < "$temp_file" | tr -d ' ')

From 9aae806f0729df2785d1a176cf1766010ffbd36a Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 16:45:37 +0100
Subject: [PATCH 07/14] fix pre-commit hook script

---
 scripts/pre-commit.sh | 89 +++++++++++++++++++++----------------------
 1 file changed, 44 insertions(+), 45 deletions(-)

diff --git a/scripts/pre-commit.sh b/scripts/pre-commit.sh
index 698b05b..fed2186 100755
--- a/scripts/pre-commit.sh
+++ b/scripts/pre-commit.sh
@@ -1,58 +1,57 @@
 #!/bin/bash
+# Pre-commit hook for Deep-MI website
+# Install: cp scripts/pre-commit.sh .git/hooks/pre-commit && chmod +x .git/hooks/pre-commit
 
-exit 0
-echo "✓ All pre-commit checks passed!"
-echo ""
+set -e
 
+echo "Running pre-commit checks..."
+
+# Check if validation scripts exist
+if [ ! -f "scripts/validate_yaml.rb" ] || [ ! -f "scripts/validate_posts.sh" ]; then
+  echo "⚠️  Validation scripts not found. Skipping validation."
+  exit 0
 fi
-  read
-  echo "Press Enter to continue anyway, or Ctrl+C to abort."
-  echo "Consider optimizing images before committing."
+
+# Validate YAML files
+echo "→ Validating YAML files..."
+if ! ./scripts/validate_yaml.rb; then
   echo ""
-  echo "$large_files"
-  echo "⚠️  Warning: Large files detected:"
-if [ -n "$large_files" ]; then
+  echo "✗ YAML validation failed!"
+  echo "  Fix the errors above before committing."
+  exit 1
+fi
 
-done)
-  fi
-    fi
-      echo "$file ($(($size / 1024))KB)"
-    if [ $size -gt 1048576 ]; then  # 1MB
-    size=$(wc -c < "$file")
-  if [ -f "$file" ]; then
-large_files=$(git diff --cached --name-only --diff-filter=ACM | while read file; do
-echo "→ Checking for large files..."
+# Validate posts
 echo ""
-# Check for large files
-
-fi
-  exit 1
-  echo "  Fix the errors above before committing."
-  echo "✗ Post validation failed!"
-  echo ""
-if ! ./scripts/validate_posts.sh; then
 echo "→ Validating posts..."
-echo ""
-# Validate posts
-
-fi
-  exit 1
-  echo "  Fix the errors above before committing."
-  echo "✗ YAML validation failed!"
+if ! ./scripts/validate_posts.sh; then
   echo ""
-if ! ./scripts/validate_yaml.rb; then
-echo "→ Validating YAML files..."
-# Validate YAML files
-
+  echo "✗ Post validation failed!"
+  echo "  Fix the errors above before committing."
+  exit 1
 fi
-  exit 0
-  echo "⚠️  Validation scripts not found. Skipping validation."
-if [ ! -f "scripts/validate_yaml.rb" ] || [ ! -f "scripts/validate_posts.sh" ]; then
-# Check if validation scripts exist
 
-echo "Running pre-commit checks..."
+# Check for large files
+echo ""
+echo "→ Checking for large files..."
+large_files=$(git diff --cached --name-only --diff-filter=ACM | while read file; do
+  if [ -f "$file" ]; then
+    size=$(wc -c < "$file")
+    if [ $size -gt 1048576 ]; then  # 1MB
+      echo "$file ($(($size / 1024))KB)"
+    fi
+  fi
+done)
 
-set -e
+if [ -n "$large_files" ]; then
+  echo "⚠️  Warning: Large files detected:"
+  echo "$large_files"
+  echo ""
+  echo "Consider optimizing images before committing."
+  echo "Press Enter to continue anyway, or Ctrl+C to abort."
+  read
+fi
 
-# Install: cp scripts/pre-commit.sh .git/hooks/pre-commit && chmod +x .git/hooks/pre-commit
-# Pre-commit hook for Deep-MI website
+echo ""
+echo "✓ All pre-commit checks passed!"
+exit 0

From eb349e397267c2253eb45ada725b5de66dfbb6fd Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Fri, 13 Feb 2026 16:57:36 +0100
Subject: [PATCH 08/14] Update QUICKSTART.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 QUICKSTART.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QUICKSTART.md b/QUICKSTART.md
index 37b79c5..8c2d000 100644
--- a/QUICKSTART.md
+++ b/QUICKSTART.md
@@ -20,7 +20,7 @@ bundle exec jekyll serve
 
 ### News Post (5 minutes)
 
-1. Create: `_posts/2026-02-13-Title.md`
+1. Create: `_posts/YYYY-MM-DD-Title.md`
 2. Copy template from: `_templates/post-template.md`
 3. Add images to: `/static/img/`
 4. Validate: `./scripts/validate_posts.sh`

From 18e8ed507b51c5969d8e2c6ccfe11c11cef1d6cb Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Fri, 13 Feb 2026 17:01:07 +0100
Subject: [PATCH 09/14] Update scripts/pre-commit.sh

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 scripts/pre-commit.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/scripts/pre-commit.sh b/scripts/pre-commit.sh
index fed2186..0f2b639 100755
--- a/scripts/pre-commit.sh
+++ b/scripts/pre-commit.sh
@@ -48,8 +48,11 @@ if [ -n "$large_files" ]; then
   echo "$large_files"
   echo ""
   echo "Consider optimizing images before committing."
-  echo "Press Enter to continue anyway, or Ctrl+C to abort."
-  read
+  # Only prompt if running interactively and not explicitly skipped
+  if [ -t 0 ] && [ -z "$SKIP_LARGE_FILE_PROMPT" ]; then
+    echo "Press Enter to continue anyway, or Ctrl+C to abort."
+    read
+  fi
 fi
 
 echo ""

From 3f055ef043dffe5e3a7333f736035a989a87127d Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 17:04:49 +0100
Subject: [PATCH 10/14] unify github path url

---
 _data/publications.yml   | 22 +++++++++++-----------
 scripts/validate_yaml.rb |  7 ++++++-
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/_data/publications.yml b/_data/publications.yml
index 07d6223..91ebf11 100644
--- a/_data/publications.yml
+++ b/_data/publications.yml
@@ -24,7 +24,7 @@
 #   arxiv: 1904.02082
 #   doi: 10.1002/mrm.28022
 #   pdf: '/static/pub/lastname_year_ifnecessarymore.pdf'
-#   github: /deep-mi/project
+#   github: deep-mi/project
 #   bibtex: '/static/pub/lastname_year_ifnecessarymore.bib'
 #   links:
 #     - name: 'Some coauthor Lab'
@@ -42,7 +42,7 @@
   arxiv: 'https://arxiv.org/abs/2505.02048'
   doi: '10.1109/TMI.2025.3650412'
   pdf: 'https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11322583'
-  github: 'deep-MI/YODA'
+  github: 'deep-mi/YODA'
 
 - id: 'pollak_2025'
   authors: '**Pollak C**, **Kügler D**, Bauer T, Rüber T, **Reuter M**'
@@ -54,7 +54,7 @@
   bibtex: '/static/pub/pollak_2025.bib'
   doi: 10.1162/imag_a_00446
   pmcid: 'PMC11917724'
-  github: 'deep-MI/LIT'
+  github: 'deep-mi/LIT'
 
 - id: 'peng_2025'
   authors: 'Xu P, **Estrada S**, Etteldorf R, Liu D, Shahid M, Zeng W, Früh D, **Reuter M**, Breteler MMB, Aziz NA'
@@ -89,7 +89,7 @@
   pdf: 'https://direct.mit.edu/imag/article-pdf/doi/10.1162/imag_a_00180/2375595/imag_a_00180.pdf'
   bibtex: '/static/pub/henschel_2024.bib'
   doi: 10.1162/imag_a_00180
-  github: /deep-mi/VINNA4neonates
+  github: deep-mi/VINNA4neonates
 
 - id: 'ewert_2024a'
   authors: '**Ewert C\***, **Kügler D\***, Stirnberg R, Koch A, Yendiki A, **Reuter M**. (\*co-first)'
@@ -102,7 +102,7 @@
   bibtex: '/static/pub/ewert_2024a.bib'
   doi: 10.1162/imag_a_00121
   pdf: 'https://direct.mit.edu/imag/article-pdf/doi/10.1162/imag_a_00121/2358010/imag_a_00121.pdf'
-  github: /deep-mi/DISCUS
+  github: deep-mi/DISCUS
 
 - id: 'estrada2023'
   authors: '**Estrada S**, **Kügler D**, Bahrami E, Xu P, Mousa D, Breteler MMB, Aziz NA, **Reuter M**'
@@ -116,7 +116,7 @@
   pmcid: 'PMC11576934'
   doi: 10.1162/imag_a_00034
   pdf: 'https://direct.mit.edu/imag/article-pdf/doi/10.1162/imag_a_00034/2182290/imag_a_00034.pdf'
-  github: /deep-mi/FastSurfer
+  github: deep-mi/FastSurfer
 
 - id: 'diers_2023'
   authors: '**Diers K**, Baumeister H, Jessen F, Düzel E, Berron D, **Reuter M**'
@@ -128,7 +128,7 @@
   bibtex: '/static/pub/diers_2023.bib'
   doi: 10.1016/j.neuroimage.2023.120182
   pdf: 'https://doi.org/10.1016/j.neuroimage.2023.120182'
-  github: 'deep-MI/Hipsta'
+  github: 'deep-mi/Hipsta'
 
 - id: 'pollak_2023b'
   authors: '**Pollak C**, **Kügler D**, Breteler MMB, **Reuter M**'
@@ -140,7 +140,7 @@
   bibtex: '/static/pub/pollak_2023b.bib'
   doi: 10.1016/j.neuroimage.2023.120176
   pdf: 'https://www.sciencedirect.com/science/article/pii/S1053811923003270/pdfft?isDTMRedir=true&download=true'
-  github: 'deep-MI/head-motion-tools'
+  github: 'deep-mi/head-motion-tools'
 
 
 - id: 'pollak_2023a'
@@ -162,7 +162,7 @@
   journal: '*NeuroImage*'
   type: 'journal'
   year: 2022
-  github: /deep-mi/FastSurfer
+  github: deep-mi/FastSurfer
   doi: 10.1016/j.neuroimage.2022.119703
   pmcid: 'PMC9771831'
   image: '/static/pub/faber_2022.jpg'
@@ -187,7 +187,7 @@
   journal: '*Medical Imaging with Deep Learning, Conference (MIDL)*'
   type: 'journal'
   year: 2022
-  github: /deep-mi/3d-neuro-seg
+  github: deep-mi/3d-neuro-seg
   image: '/static/pub/roy_2022.png'
   pdf: 'https://openreview.net/pdf?id=Ob62JPB_CDF'
   bibtex: '/static/pub/roy_2022.bib'
@@ -203,7 +203,7 @@
   arxiv: 2112.09654
   pmcid: 'PMC9801435'
   image: '/static/pub/henschel_2022.jpg'
-  github: /deep-mi/FastSurfer
+  github: deep-mi/FastSurfer
   doi: 10.1016/j.neuroimage.2022.118933
   pdf: 'https://www.sciencedirect.com/science/article/pii/S1053811922000623/pdfft?md5=0522f6a35232c9e9e57674816ce19a7a&pid=1-s2.0-S1053811922000623-main.pdf'
   bibtex: '/static/pub/henschel_2022.bib'
diff --git a/scripts/validate_yaml.rb b/scripts/validate_yaml.rb
index 54057cf..c15492c 100755
--- a/scripts/validate_yaml.rb
+++ b/scripts/validate_yaml.rb
@@ -8,7 +8,12 @@ def validate_file(filepath)
   puts "Validating #{filepath}..."
 
   begin
-    data = YAML.safe_load_file(filepath, permitted_classes: [Date, Time], aliases: true)
+    # Use safe_load_file for Ruby >= 3.1, fall back to load_file for older versions
+    data = if YAML.respond_to?(:safe_load_file)
+      YAML.safe_load_file(filepath, permitted_classes: [Date, Time], aliases: true)
+    else
+      YAML.load_file(filepath)
+    end
 
     # File-specific validations
     case File.basename(filepath)

From 3683cc3cae100e1f842a718820e2d83c47d4bc26 Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 17:07:31 +0100
Subject: [PATCH 11/14] make validate-yaml work from any dir

---
 _templates/publication-template.md |  4 +++-
 scripts/validate_yaml.rb           | 14 ++++++++++----
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/_templates/publication-template.md b/_templates/publication-template.md
index 60fc5e9..57da04b 100644
--- a/_templates/publication-template.md
+++ b/_templates/publication-template.md
@@ -20,7 +20,7 @@ Copy this template when adding a new publication to `_data/publications.yml`
   arxiv: '2401.12345'  # optional - arXiv ID
   doi: '10.1234/journal.2024.123456'  # strongly recommended
   pdf: 'https://journal.com/paper.pdf'  # or '/static/pub/lastname_year.pdf'
-  github: 'deep-mi/repository-name'  # optional - relative to github.com
+  github: 'deep-mi/repository-name'  # optional - format: org/repo (no leading slash)
   bibtex: '/static/pub/lastname_year.bib'
   links:  # optional - additional links
     - name: 'Project Website'
@@ -51,5 +51,7 @@ Copy this template when adding a new publication to `_data/publications.yml`
 - Always include DOI if available
 - Bold current and former lab members in author list
 - Keep image file size small (max 100KB)
+- GitHub format: `'deep-mi/repository-name'` (lowercase org, no leading slash)
+  - Rendered as: `https://github.com/deep-mi/repository-name`
 - Test that all file paths exist before committing
 
diff --git a/scripts/validate_yaml.rb b/scripts/validate_yaml.rb
index c15492c..c505296 100755
--- a/scripts/validate_yaml.rb
+++ b/scripts/validate_yaml.rb
@@ -4,6 +4,9 @@
 require 'yaml'
 require 'date'
 
+# Get the project root directory (parent of scripts directory)
+PROJECT_ROOT = File.expand_path('..', __dir__)
+
 def validate_file(filepath)
   puts "Validating #{filepath}..."
 
@@ -41,8 +44,8 @@ def validate_members(data, filepath)
       end
     end
 
-    # Check if image file exists
-    image_path = File.join(File.dirname(__dir__), member['image'])
+    # Check if image file exists (resolve relative to project root)
+    image_path = File.expand_path(member['image'], PROJECT_ROOT)
     unless File.exist?(image_path)
       puts "  Warning: Image not found for #{member['name']}: #{member['image']}"
     end
@@ -80,12 +83,12 @@ def validate_publications(data, filepath)
       raise "Publication #{pub['id']} has invalid year: #{pub['year']}"
     end
 
-    # Check if files exist
+    # Check if files exist (resolve relative to project root)
     ['image', 'bibtex', 'pdf'].each do |file_field|
       next unless pub[file_field]
       next if pub[file_field].start_with?('http')
 
-      file_path = File.join(File.dirname(__dir__), pub[file_field])
+      file_path = File.expand_path(pub[file_field], PROJECT_ROOT)
       unless File.exist?(file_path)
         puts "  Warning: File not found for #{pub['id']}: #{pub[file_field]}"
       end
@@ -96,6 +99,9 @@ def validate_publications(data, filepath)
 # Main execution
 exit_code = 0
 
+# Change to project root directory to find _data files
+Dir.chdir(PROJECT_ROOT)
+
 Dir.glob('_data/*.yml').each do |file|
   unless validate_file(file)
     exit_code = 1

From 0173170e594dac4315fa6de646373314fc485e1a Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 17:17:31 +0100
Subject: [PATCH 12/14] backup images and cleanup

---
 scripts/optimize_images.sh | 178 ++++++++++++++++++++++++++++++++++---
 1 file changed, 166 insertions(+), 12 deletions(-)

diff --git a/scripts/optimize_images.sh b/scripts/optimize_images.sh
index 5d26b9e..5883199 100755
--- a/scripts/optimize_images.sh
+++ b/scripts/optimize_images.sh
@@ -10,6 +10,66 @@ GREEN='\033[0;32m'
 YELLOW='\033[1;33m'
 NC='\033[0m' # No Color
 
+# Array to track temporary files for cleanup
+TEMP_FILES=()
+
+# Array to track backup files
+BACKUP_FILES=()
+
+# Cleanup function
+cleanup() {
+    if [ ${#TEMP_FILES[@]} -gt 0 ]; then
+        for temp_file in "${TEMP_FILES[@]}"; do
+            if [ -f "$temp_file" ]; then
+                rm -f "$temp_file"
+            fi
+        done
+    fi
+}
+
+# Set up trap to cleanup on exit or error
+trap cleanup EXIT ERR INT TERM
+
+# Function to create backup
+create_backup() {
+    local input_file="$1"
+    local backup_file="${input_file}.backup"
+
+    if cp "$input_file" "$backup_file" 2>/dev/null; then
+        BACKUP_FILES+=("$backup_file")
+        return 0
+    else
+        echo -e "  ${RED}✗ Error: Failed to create backup${NC}"
+        return 1
+    fi
+}
+
+# Function to restore from backup
+restore_backup() {
+    local input_file="$1"
+    local backup_file="${input_file}.backup"
+
+    if [ -f "$backup_file" ]; then
+        mv "$backup_file" "$input_file"
+        # Remove from backup tracking
+        BACKUP_FILES=("${BACKUP_FILES[@]/$backup_file}")
+        return 0
+    fi
+    return 1
+}
+
+# Function to remove backup
+remove_backup() {
+    local input_file="$1"
+    local backup_file="${input_file}.backup"
+
+    if [ -f "$backup_file" ]; then
+        rm -f "$backup_file"
+        # Remove from backup tracking
+        BACKUP_FILES=("${BACKUP_FILES[@]/$backup_file}")
+    fi
+}
+
 # Check if ImageMagick is installed
 if ! command -v magick &> /dev/null && ! command -v convert &> /dev/null; then
     echo -e "${RED}Error: ImageMagick is not installed${NC}"
@@ -34,17 +94,41 @@ optimize_member_photo() {
     local filename=$(basename "$input_file")
     local temp_file="${input_file}.tmp.jpg"
 
+    # Add to cleanup list
+    TEMP_FILES+=("$temp_file")
+
     echo -e "${YELLOW}Processing member photo: $filename${NC}"
 
+    # Check if input file exists and is readable
+    if [ ! -f "$input_file" ]; then
+        echo -e "  ${RED}✗ Error: File not found: $input_file${NC}"
+        return 1
+    fi
+
+    if [ ! -r "$input_file" ]; then
+        echo -e "  ${RED}✗ Error: File not readable: $input_file${NC}"
+        return 1
+    fi
+
+    # Create backup before processing
+    if ! create_backup "$input_file"; then
+        return 1
+    fi
+
     # Resize to 365x365 if needed, set to 72 DPI, and compress
-    $CONVERT_CMD "$input_file" \
+    if ! $CONVERT_CMD "$input_file" \
         -resize 365x365^ \
         -gravity center \
         -extent 365x365 \
         -density 72 \
         -quality 85 \
         -strip \
-        "$temp_file"
+        "$temp_file" 2>/dev/null; then
+        echo -e "  ${RED}✗ Error: Failed to process image (possibly corrupt or invalid format)${NC}"
+        rm -f "$temp_file"
+        restore_backup "$input_file"
+        return 1
+    fi
 
     # Check file size
     size=$(wc -c < "$temp_file" | tr -d ' ')
@@ -53,13 +137,23 @@ optimize_member_photo() {
     if [ $size_kb -gt 100 ]; then
         echo -e "  ${YELLOW}Warning: ${filename} is ${size_kb}KB (max 100KB)${NC}"
         echo -e "  Attempting further compression..."
-        $CONVERT_CMD "$temp_file" -quality 75 "$temp_file"
+        if ! $CONVERT_CMD "$temp_file" -quality 75 "$temp_file" 2>/dev/null; then
+            echo -e "  ${RED}✗ Error: Failed to compress image${NC}"
+            rm -f "$temp_file"
+            restore_backup "$input_file"
+            return 1
+        fi
         size=$(wc -c < "$temp_file" | tr -d ' ')
         size_kb=$((size / 1024))
     fi
 
     mv "$temp_file" "$input_file"
-    echo -e "  ${GREEN}✓ Optimized: ${size_kb}KB${NC}"
+    # Remove from cleanup list after successful move
+    TEMP_FILES=("${TEMP_FILES[@]/$temp_file}")
+    # Remove backup after successful optimization
+    remove_backup "$input_file"
+    echo -e "  ${GREEN}✓ Optimized: ${size_kb}KB (backup removed)${NC}"
+    return 0
 }
 
 # Function to optimize publication teasers
@@ -68,14 +162,38 @@ optimize_pub_teaser() {
     local filename=$(basename "$input_file")
     local temp_file="${input_file}.tmp.jpg"
 
+    # Add to cleanup list
+    TEMP_FILES+=("$temp_file")
+
     echo -e "${YELLOW}Processing publication teaser: $filename${NC}"
 
+    # Check if input file exists and is readable
+    if [ ! -f "$input_file" ]; then
+        echo -e "  ${RED}✗ Error: File not found: $input_file${NC}"
+        return 1
+    fi
+
+    if [ ! -r "$input_file" ]; then
+        echo -e "  ${RED}✗ Error: File not readable: $input_file${NC}"
+        return 1
+    fi
+
+    # Create backup before processing
+    if ! create_backup "$input_file"; then
+        return 1
+    fi
+
     # Resize to max height 200px and compress
-    $CONVERT_CMD "$input_file" \
+    if ! $CONVERT_CMD "$input_file" \
         -resize x200\> \
         -quality 85 \
         -strip \
-        "$temp_file"
+        "$temp_file" 2>/dev/null; then
+        echo -e "  ${RED}✗ Error: Failed to process image (possibly corrupt or invalid format)${NC}"
+        rm -f "$temp_file"
+        restore_backup "$input_file"
+        return 1
+    fi
 
     # Check file size
     size=$(wc -c < "$temp_file" | tr -d ' ')
@@ -84,13 +202,23 @@ optimize_pub_teaser() {
     if [ $size_kb -gt 100 ]; then
         echo -e "  ${YELLOW}Warning: ${filename} is ${size_kb}KB (max 100KB)${NC}"
         echo -e "  Applying maximum compression..."
-        $CONVERT_CMD "$temp_file" -quality 70 "$temp_file"
+        if ! $CONVERT_CMD "$temp_file" -quality 70 "$temp_file" 2>/dev/null; then
+            echo -e "  ${RED}✗ Error: Failed to compress image${NC}"
+            rm -f "$temp_file"
+            restore_backup "$input_file"
+            return 1
+        fi
         size=$(wc -c < "$temp_file" | tr -d ' ')
         size_kb=$((size / 1024))
     fi
 
     mv "$temp_file" "$input_file"
-    echo -e "  ${GREEN}✓ Optimized: ${size_kb}KB${NC}"
+    # Remove from cleanup list after successful move
+    TEMP_FILES=("${TEMP_FILES[@]/$temp_file}")
+    # Remove backup after successful optimization
+    remove_backup "$input_file"
+    echo -e "  ${GREEN}✓ Optimized: ${size_kb}KB (backup removed)${NC}"
+    return 0
 }
 
 # Main script
@@ -116,25 +244,51 @@ case "$1" in
     all-members)
         echo "Optimizing all member photos..."
         echo ""
+        success_count=0
+        error_count=0
         for img in static/img/members/*.jpg; do
             if [ -f "$img" ]; then
-                optimize_member_photo "$img"
+                if optimize_member_photo "$img"; then
+                    ((success_count++))
+                else
+                    ((error_count++))
+                fi
             fi
         done
         echo ""
-        echo -e "${GREEN}✓ All member photos optimized!${NC}"
+        if [ $error_count -eq 0 ]; then
+            echo -e "${GREEN}✓ All member photos optimized! ($success_count processed)${NC}"
+        else
+            echo -e "${YELLOW}⚠ Completed with errors: $success_count succeeded, $error_count failed${NC}"
+            exit 1
+        fi
         ;;
 
     all-pubs)
         echo "Optimizing all publication teasers..."
         echo ""
+        success_count=0
+        error_count=0
         for img in static/pub/*.jpg; do
             if [ -f "$img" ]; then
-                optimize_pub_teaser "$img"
+                if optimize_pub_teaser "$img"; then
+                    ((success_count++))
+                else
+                    ((error_count++))
+                fi
             fi
         done
         echo ""
-        echo -e "${GREEN}✓ All publication teasers optimized!${NC}"
+        if [ $error_count -eq 0 ]; then
+            echo -e "${GREEN}✓ All publication teasers optimized! ($success_count processed)${NC}"
+        else
+            echo -e "${YELLOW}⚠ Completed with errors: $success_count succeeded, $error_count failed${NC}"
+            if [ ${#BACKUP_FILES[@]} -gt 0 ]; then
+                echo -e "${YELLOW}⚠ ${#BACKUP_FILES[@]} backup file(s) retained due to errors${NC}"
+                echo -e "  To restore, run: mv <file>.backup <file>"
+            fi
+            exit 1
+        fi
         ;;
 
     *)

From 8550f84f77015c27d795d8e8c923367a78aae7e1 Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 17:25:36 +0100
Subject: [PATCH 13/14] path resolution fix

---
 scripts/validate_posts.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/validate_posts.sh b/scripts/validate_posts.sh
index 9e81ccd..006ce8d 100755
--- a/scripts/validate_posts.sh
+++ b/scripts/validate_posts.sh
@@ -23,9 +23,10 @@ for file in _posts/*.md; do
   fi
 
   # Extract and validate date
+  # Try GNU date (Linux) or BSD date (macOS) - either one succeeding is valid
   date_part="${filename:0:10}"
-  if ! date -d "$date_part" "+%Y-%m-%d" > /dev/null 2>&1 && \
-     ! date -j -f "%Y-%m-%d" "$date_part" > /dev/null 2>&1; then
+  if ! ( date -d "$date_part" "+%Y-%m-%d" >/dev/null 2>&1 || \
+         date -j -f "%Y-%m-%d" "$date_part" >/dev/null 2>&1 ); then
     echo "✗ Invalid date in filename: $filename"
     ((error_count++))
     continue

From 8165d3192daaa1726d137cc32d17dbf0b6d826c1 Mon Sep 17 00:00:00 2001
From: Martin Reuter <reuter@mit.edu>
Date: Fri, 13 Feb 2026 17:34:43 +0100
Subject: [PATCH 14/14] add description to install imagemagick

---
 CONTRIBUTING.md            |  9 ++++++++-
 QUICKSTART.md              |  7 ++++++-
 README.md                  |  5 ++++-
 scripts/optimize_images.sh | 24 +++++++++++++++++++++++-
 4 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index d029274..137baba 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -118,7 +118,14 @@ Optimize images to meet size requirements:
 ./scripts/optimize_images.sh all-pubs
 ```
 
-**Requirements**: ImageMagick (`brew install imagemagick`)
+**Requirements**: ImageMagick
+
+**Installation**:
+- macOS: `brew install imagemagick`
+- Ubuntu/Debian: `sudo apt-get install imagemagick`
+- Fedora/RHEL: `sudo yum install imagemagick` or `sudo dnf install imagemagick`
+- Arch Linux: `sudo pacman -S imagemagick`
+- Windows: Download from [imagemagick.org](https://imagemagick.org/script/download.php#windows) or use `choco install imagemagick`
 
 ### Pre-commit Hook
 
diff --git a/QUICKSTART.md b/QUICKSTART.md
index 8c2d000..9fb316c 100644
--- a/QUICKSTART.md
+++ b/QUICKSTART.md
@@ -99,11 +99,16 @@ rbenv local 3.1.0
 
 ### Images too large
 ```bash
-# Optimize automatically
+# Optimize automatically (requires ImageMagick)
 ./scripts/optimize_images.sh member static/img/members/photo.jpg
 ./scripts/optimize_images.sh pub static/pub/teaser.jpg
 ```
 
+**Install ImageMagick**:
+- macOS: `brew install imagemagick`
+- Linux: `sudo apt-get install imagemagick` or `sudo yum install imagemagick`
+- Windows: [imagemagick.org](https://imagemagick.org/script/download.php#windows)
+
 ## Useful Commands
 
 ```bash
diff --git a/README.md b/README.md
index af94cfb..6a77f73 100644
--- a/README.md
+++ b/README.md
@@ -69,7 +69,10 @@ See `CONTRIBUTING.md` for detailed contribution guidelines.
 ./scripts/optimize_images.sh pub static/pub/paper_id.jpg
 ```
 
-Requires ImageMagick: `brew install imagemagick`
+**Requirements**: ImageMagick
+- macOS: `brew install imagemagick`
+- Linux: `sudo apt-get install imagemagick` or `sudo yum install imagemagick`
+- Windows: See [imagemagick.org](https://imagemagick.org/script/download.php#windows)
 
 ### Pre-commit Hook
 
diff --git a/scripts/optimize_images.sh b/scripts/optimize_images.sh
index 5883199..54782b4 100755
--- a/scripts/optimize_images.sh
+++ b/scripts/optimize_images.sh
@@ -73,7 +73,29 @@ remove_backup() {
 # Check if ImageMagick is installed
 if ! command -v magick &> /dev/null && ! command -v convert &> /dev/null; then
     echo -e "${RED}Error: ImageMagick is not installed${NC}"
-    echo "Install it with: brew install imagemagick"
+    echo ""
+    echo "Please install ImageMagick for your platform:"
+    echo ""
+    echo "  macOS:"
+    echo "    brew install imagemagick"
+    echo ""
+    echo "  Ubuntu/Debian Linux:"
+    echo "    sudo apt-get update"
+    echo "    sudo apt-get install imagemagick"
+    echo ""
+    echo "  Fedora/RHEL/CentOS Linux:"
+    echo "    sudo yum install imagemagick"
+    echo "    # or on newer systems:"
+    echo "    sudo dnf install imagemagick"
+    echo ""
+    echo "  Arch Linux:"
+    echo "    sudo pacman -S imagemagick"
+    echo ""
+    echo "  Windows:"
+    echo "    Download from: https://imagemagick.org/script/download.php#windows"
+    echo "    Or use Chocolatey: choco install imagemagick"
+    echo "    Or use Scoop: scoop install imagemagick"
+    echo ""
     exit 1
 fi