macOS compile modkit - v0.6.3

[SuhasSrinivasan]

1. Updated help markdown in book/src/mac_compile_modkit.md
2. No MPS support and no Python and PyTorch dependencies are the default build options
3. If MPS support is needed user can run MODKIT_MPS_SUPPORT=1 bash mac_compile_modkit.sh
4. Installs Xcode Command Line Tools
5. Installs Homebrew package manager
6. Considers uv and pyenv through config (if MODKIT_MPS_SUPPORT=1)
7. Installs rustup (Rust toolchain installer)
8. Installs Rust compiler (rustc) and Cargo build tool
9. Clones the modkit GitHub repository
10. Checks out the latest release version
11. Creates a Python virtual environment (if MODKIT_MPS_SUPPORT=1)
12. Installs PyTorch in the virtual environment (if MODKIT_MPS_SUPPORT=1)
13. Sets and verifies environment variables for libtorch (if MODKIT_MPS_SUPPORT=1)
14. Verifies modkit binary is working and prints installation info

[Copilot]

Pull request overview

Adds a macOS (Apple Silicon) install/compile path for modkit via a new automation script and accompanying documentation, aiming to make MPS (Metal) GPU-enabled builds opt-in.

Changes:

• Added mac_compile_modkit.sh to automate dependency installation, repo checkout, optional Python/PyTorch setup, and building modkit.
• Added mdBook documentation page and nav entry describing macOS compilation and MPS/Python controls.
• Updated README.md to point users to the new macOS compilation path.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 9 comments.

File	Description
README.md	Adds a macOS (Apple Silicon) section pointing to the new script and guide.
mac_compile_modkit.sh	New end-to-end macOS installer/compiler script with optional MPS/PyTorch support.
book/src/SUMMARY.md	Adds the new macOS compilation page to the mdBook navigation.
book/src/mac_compile_modkit.md	New documentation page explaining script usage, options, and troubleshooting.

Comments suppressed due to low confidence (2)

mac_compile_modkit.sh:819

• Same issue as above: in a sourced script $0 refers to the parent shell, so the usage guidance is inaccurate. Prefer ${BASH_SOURCE[0]} (or equivalent) for usage text in this generated script.

if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
    echo "Error: This script must be sourced, not executed."
    echo "Usage: source ${0} <installation_directory> [--verbose]"
    exit 1

book/src/mac_compile_modkit.md:150

• These MPS rebuild instructions use cargo build --features accelerate,tch from the repo root, but the workspace root is a virtual manifest and the modkit package itself doesn't define these features. As written, this command will fail. Please update to the correct build invocation for this workspace that produces an MPS-enabled open-chromatin build.

source ~/tools/setup_modkit_env.sh ~/tools
cd ~/tools/modkit
cargo clean
cargo build --release --features accelerate,tch

</details>



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