mac setup

Basics

1. Install homebrew for package management.
2. Replace terminal with iTerm2.
3. oh-my-zsh to configure zsh.
4. `defaults write com.apple.finder AppleShowAllFiles YES
5. Connect GitHub account with ssh brew install:

• git
• eza to make ls and tree prettier. Eric Ma’s essay has a list of other useful terminal hacks.
  • Add alias ls='eza --long --git --header --group' and alias tree='eza --tree --level=2 --long --header --git' to .zshrc
• imagemagick to manipulate images into other formats
• stats to see system stats

Code

brew install --cask:

• R
  • I would recommend only installing renv into your base distribution, and then using renv for virtual environments for each individual project. This creates a renv.lock file which tells users exactly which version of each package you used for the analysis, making the research more reproducible.
  • Most people use RStudio, but I use VSCode. For use with VSCode and the VScode-R extension, you will also need to install languageserver, jsonlite, rlang. For an enhanced experience, install radian, edit the Rterm path and enable bracketed paste (and maybe add an argument to r.rterm.option)
  • I created a cookiecuttertemplate for R analysis projects.
• Quarto for technical documents
• python (uv for python versioning and virtual environments)
  • Formerly used pyenv, venv, pip but uv replaces all of these
  • Former conda/mamba/micromamba user, trying out the recommended stuff before probably switching to pixi. Further notes on python versioning, virtual environments and packaging.
• obsidian
  • daily notes in notes/daily with template templates/daily. template folder templates/
  • community plugins
    • advanced tables
    • auto note mover (exclude notes/daily)
    • clear unused images
    • code block enhancer (ignore todoist)
    • dataview
    • git
    • github publisher (with quartz and github pages for site)
    • homepage
    • linter
    • minimal theme
    • paste URL into section
    • quick latex
    • rollover daily todos
    • tasks
    • templater
  • matcha to pull my rss feeds, all situated in a folder feed/

Applications

brew install --cask :

• VSCode IDE. I use VSCode for everything because I can have one environment for all programming languages.
  • Citation Picker for Zotero, Code Spell Checker, Excel Viewer, GitHub Copilot, Markdown All in One, markdownlint, python, quarto, R, Rainbow CSV, White theme, stan-vscode, vscode-pdf, gitlens, autodocstring, TODOtree, ruff
  • Settings. Terminal › External: Osx Exec: iTerm.app
• bitwardenpassword manager.
• Zotero reference management.
  • Better BibTex extension
• Arc browser. Trying this one – I used Brave before.
  • bitwarden extension
  • Zotero Connector extension
  • Refined GitHub extension
• Optional: docker, zoom, microsoft office

Themes and colours

Mostly inspired by the Hundred Rabbits artist collective and their site. My website is also inspired by them (see style.css).

• oh-my-zsh. ZSH_THEME="minimal"
• VSCode. White theme.
• Obsidian. Minimal theme. Monochrome palette:
• ["#FBFBFB", "#222222", "#777777", "#727272"]

See also How to Set up an Apple Mac for Software Development.