Mac compile script based on v0.6.2

[SuhasSrinivasan]

0. Added help markdown to book/src
1. Installs Xcode Command Line Tools
2. Installs Homebrew package manager
3. Considers uv and pyenv through config
4. Installs rustup (Rust toolchain installer)
5. Installs Rust compiler (rustc) and Cargo build tool
6. Clones the modkit GitHub repository
7. Checks out the latest release version
8. Creates a Python virtual environment
9. Installs PyTorch in the virtual environment
10. Sets and verifies environment variables for libtorch
11. Builds modkit with macOS GPU (MPS) support

[Copilot]

Pull request overview

This PR adds a macOS-focused installation path for building modkit from source with the tch/PyTorch-backed open-chromatin stack, plus companion documentation in the mdBook docs. It fits into the existing repository by extending the current build-note/docs story with a scripted Apple/macOS workflow.

Changes:

• Adds a new mac_compile_modkit.sh installer that sets up toolchains, clones the repo, prepares Python/PyTorch, and builds modkit.
• Adds configurable Python selection via system Python, pyenv, or uv.
• Adds a new mdBook page describing the macOS installation workflow and troubleshooting steps.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 12 comments.

File	Description
mac_compile_modkit.sh	New end-to-end macOS build/install script for compiling modkit with PyTorch/libtorch-based support.
book/src/mac_compile_modkit.md	New user-facing documentation for the macOS installation workflow and common troubleshooting steps.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[SuhasSrinivasan]

Tested on Sunday, May 3, 2026 at 7:30PM PDT
macOS: 26.4.1
M2 Ultra Mac Studio

$ bash mac_compile_modkit.sh ~/projects/modkit/modkit-0.6.2 v0.6.2
.
.
.
   Compiling modkit v0.6.1 (/Users/suhas/projects/modkit/modkit-0.6.2/modkit/modkit)
    Finished `release` profile [optimized] target(s) in 1m 45s
✓ Modkit compiled successfully!
✓ Binary created at: /Users/suhas/projects/modkit/modkit-0.6.2/modkit/target/release/modkit
  Binary size:  21M

Testing modkit binary...
modkit 0.6.1
✓ Modkit is working correctly!

Available modkit commands:
Installation information saved to: /Users/suhas/projects/modkit/modkit-0.6.2/installation_info.txt
✓ Added modkit environment setup to ~/.zprofile
  It will activate automatically in every new terminal session.

Total installation time: 2 minutes 39 seconds

Versioning issue noted in #614