ome-ngff-samples

This is a page to list various OME-NGFF sample images from IDR. Deployed at https://idr.github.io/ome-ngff-samples/

Development

Prerequisites

• pixi - Cross-platform package management tool

Local Development

1. Install dependencies:

   pixi install

2. Start the development server:

   pixi run serve

   The site will be available at http://127.0.0.1:4000/ome-ngff-samples/

3. Build the static site:

   pixi run build

   The built site will be in the _site/ directory.

How It Works

• pixi manages the Ruby environment and dependencies
• Jekyll 4.0 builds the static site
• Minima 2.5.2 theme with custom head support for jQuery/DataTables
• Both local and CI use the same pixi.toml and Gemfile.lock for consistency

Deployment

The site is automatically deployed to GitHub Pages when changes are pushed to the main branch using GitHub's built-in Jekyll build process.

Troubleshooting

Permission denied errors with pixi on macOS

If you encounter permission denied errors with your temp directory when running pixi commands:

mkdir -p ~/tmp
export TMPDIR=~/tmp

To make this permanent, add to your shell profile:

echo 'export TMPDIR=~/tmp' >> ~/.zshrc  # or ~/.bashrc

This is particularly common on university/enterprise-managed macOS machines where the default $TMPDIR may have restricted permissions.