feat: Use locked Pixi environment for Binder deployment

[matthewfeickert]

• Use binder/postBuild pattern to install conda explicit spec export of Pixi environment into Binder conda environment.
• Remove binder/apt.txt and binder/requirements.txt.
• Update book/introduction.md to note that for pip or uv users the dependencies are in book/requirements.txt.

[Copilot]

Pull request overview

This PR modernizes the Binder deployment by using a locked Pixi environment instead of manually maintained requirements files. It installs Pixi during the Binder build and exports a conda explicit spec from the Pixi workspace to ensure environment reproducibility. The changes also update Python to 3.13 and consolidate dependency management.

Key changes:

• Adds jq as a conda dependency in pixi.toml (previously in binder/apt.txt)
• Implements a new Binder build approach using Pixi workspace export to conda explicit spec
• Updates book/requirements.txt with current dependency versions for pip/uv users

Reviewed changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
pixi.toml	Added jq as a dependency to replace the apt package
pixi.lock	Lock file updates for jq and its dependency oniguruma across all platforms
book/requirements.txt	Updated from minimal jupyter-book spec to full dependency list for pip users
book/introduction.md	Updated documentation to reference book/requirements.txt instead of binder/requirements.txt
binder/runtime.txt	Updated Python version from 3.12 to 3.13
binder/requirements.txt	Removed (dependencies now managed through Pixi)
binder/postBuild	Replaced ROOT installation with Pixi-based workflow
binder/apt.txt	Removed (jq now installed via conda)

Comments suppressed due to low confidence (1)

binder/postBuild:6

• Installing Pixi via curl in the postBuild script introduces a potential security risk and build reproducibility concern. The script downloads and executes code without verification. Consider:

1. Pinning to a specific Pixi version
2. Verifying the checksum of the downloaded installer
3. Or pre-installing Pixi in the base Binder image if possible

curl -fsSL https://pixi.sh/install.sh | sh

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[Copilot]

The tilde (~) in the PATH export will not expand to the home directory because it's inside double quotes. This should use $HOME instead:

export PATH="$HOME/.pixi/bin:${PATH}"

Suggested change

	export PATH="~/.pixi/bin:${PATH}"
	export PATH="$HOME/.pixi/bin:${PATH}"

[Copilot]

Sourcing ~/.bashrc won't work reliably in non-interactive scripts. The Pixi installation typically modifies .bashrc for interactive shells only. Consider using the Pixi binary path directly by setting the PATH immediately after installation without relying on shell configuration files.

Suggested change

	. ~/.bashrc
	# Sourcing ~/.bashrc doesn't seem to pick up changes, so manually set PATH
	export PATH="~/.pixi/bin:${PATH}"
	# Removed sourcing of ~/.bashrc; set PATH directly instead
	export PATH="$HOME/.pixi/bin:${PATH}"