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Setup a computer (macOS)

  • Include explanation about both Intel and arm

General

How to clean install

Misc

  • zsh: in general use zshrc equivalent to bash_profile

Before starting clean install

List an app

ls -la /Applications/ > InstalledAppsTerminal.txt
  • List of brew installed stuff
brew leaves > brew_leaves.txt
brew list > brew_list.txt

Google Chrome OneTab

  • Export URLs

Clean install procedure

  • Install the newest version of macOS if necessary
  • Restart with recovery mode
    • Intel: Command + R
    • Apple:
  • Open disk utility
    • Erase "Macintosh HD" WITHOUT Data, which includes both "Macintosh HD" and "MAcintosh HD - Data" and reformat it
      • Click Erase. However, if you see an Erase Volume Group button, click that button instead.
    • (maybe not needed) Erase "Macintosh HD - Data" using the minus button
  • Reintall macOS
  • Reference here

After clean install

Avast, Google Chrome, Firefox

  • Follow the instruction
  • Google Chrome: use google account to sync
  • Firefox: install AdBlocker for YouTube (maybe not Enhancer for YouTube)

Misc

  • Google日本語入力
  • Finderpath

Download Xcode

  • Do not download from Apple Store
  • Download it from https://developer.apple.com/download/all/. Choose the newest version for your macOS
  • Unpack with xip -x Xcode.xxx.xip
  • Drag the unpacked application to Application folder
  • Install xcode command line tools from the same URL

brew

  • Install following their website
  • Export brew installed packages (here): brew leaves > brew_leaves.txt and brew list > brew_list.txt
  • Install exported brew installed packages (here): for i in $(cat brew_leaves); do; brew install "$i"; done
  • homebrew-cask might be useful but won't use for now (here or here)

zsh

  • Check my Evernote note
  • What to install:
$ brew install zsh-completions
$ brew install zsh-autosuggestions

Google drive

  • Download "Backup and Sync"
  • Sync
  • Change the local folder name to "GoogleDrive"
    • Pause "Backup and Sync"
    • Change file name "GoogleDrive"
    • Restart "Backup and Sync"
    • Relocate the file to "GoogleDrive"

GlobalProtect

  • MIT VPN
  • Portal address: gpvpn.mit.edu

Zotero

  • Sync with existing account
  • Make sure to check Google drive setup and the path is corrects
    • The folder name should be "GoogleDrive"
  • Misc settings:
    • Under "General": Uncheck "Automatically attach associated PDFs and ..." to avoid downloading PDF files
    • Under "General": Check linked files
    • Under "Sync": Uncheck "Sync fill-text context"
  • Install better bibtex (citation key format: [auth:lower][year])
  • Refresh citation key

R

  • Install XQuartz
  • Install gfortran https://github.com/fxcoudert/gfortran-for-macOS/releases
  • Install xz (and maybe pcre2) with brew
  • Find binariles of R builds for macOS
    • Intel: https://cloud.r-project.org/bin/macosx/base/
    • Apple silicon: https://cran.r-project.org/bin/macosx/big-sur-arm64/base/
  • To change language setting, write export LC_ALL=en_US.UTF-8 in ~/.bash_profile and $ source ~/.bash_profile or in ~./.zshrc.
  • For trouble shooting, Step 1 to 4 of this guidance solved in M2 Mac here
  • For data.table, check Shusei's tips or here

Reinstall packages

# modified from http://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-version-of-r-on-windows
# from https://gist.github.com/florianhartig/10527319

# run on old computer / r version
setwd("/Users/tomoyasasaki/GoogleDrive/admin/computer/") # or any other existing temp directory
packages <- installed.packages()[,"Package"]
save(packages, file = "Rpackages")

# run on new computer / r version
# setwd("/Users/Florian/Dropbox/temp") # or any other existing temp directory
setwd("/Users/tomoyasasaki/GoogleDrive/admin/computer/") # or any other existing temp directory
load("Rpackages")
for (p in setdiff(packages, installed.packages()[,"Package"]))
install.packages(p)

Fast R computation

  • https://mpopov.com/blog/2021/10/10/even-faster-matrix-math-in-r-on-macos-with-m1/
  • https://groups.google.com/g/r-sig-mac/c/YN6uNYCIZK0
  • https://thomasmcrow.com/blog/2021-08-optimized-blas-in-r/

radian

  • After installed Python
  • Check here
  • Set PATH for radian
export PATH=/Users/tomoyasasaki/Library/Python/3.9/bin:$PATH
  • Set r for radian and R will be stay as it is
alias r="radian"

Misc

  • Fast matrix calculation here

Python

  1. Install pyenv
  2. Install python with pyenv
  3. Install pyenv-virtualenv
  4. Install pip in one of your environment

pyenv

  • Check here
  • Thanks to Shusei (here)
  • Also check here
  • Install with brew install pyenv
  • In .bash_profile or .zshrc
PS1="%1~ \$ "
#export PYENV_ROOT="/User/tomoyasasaki/.pyenv"
export PYENV_VIRTUALENV_DISABLE_PROMPT=1
if which pyenv > /dev/null; then eval "$(pyenv init -)"; fi
if which pyenv-virtualenv-init > /dev/null; then eval "$(pyenv virtualenv-init -)"; fi
eval "$(pyenv init --path)"
eval "$(pyenv virtualenv-init -)"
#eval "$(pyenv init -)"
  • In .zshrc
echo 'eval "$(pyenv init --path)"' >> ~/.zprofile
  • Install available python version pyenv install -l
  • Install python version with pyenv install [ver]

pyenv-virtualenv

  • More convenient to control multiple versions
  • You can also use pyenv-virtualenv: brew install pyenv-virtualenv
    • New environment: pyenv virtualenv [ver] [envname]
    • Activate environment: pyenv activate [envname]
    • Deactivate environment: pyenv deactivate

pip

curl -sSL https://bootstrap.pypa.io/get-pip.py -o get-pip.py
# In one of your pyenv-virutalenv environments,
python get-pip.py
  • Save and reinstall pip installed package (here, here)
  • Problem of freeze (here)
  • (Probably) no need to check for each enviornment
pip freeze > /path/to/requirements.txt
pip install -r /path/to/requirements.txt

Tex

  • Old procedure (still works though)
    • Install ghostscript with brew brew install ghostscript
    • Download MacTex and custom install without ghostscript
  • Updated
    • Download MacTex with brew brew install --cask mactex
    • Update packages with sudo tlmgr update --self --all
    • Reference here

DBeaver

  • Download from here
  • Setup connection for databases

VS Code

  • Setup extensions
  • Remote SSH extension can connect various remote machines via VS Code

Git

  • Use git from brew (here): brew install git
  • If on Intel, add export PATH="/usr/local/bin:${PATH}"
  • If on ARM/M1, add export PATH="/opt/homebrew/bin:${PATH}"
  • Setup email for commit: git config --global user.email "[email protected]"

Github

  • Connect github with new credential or ssh

Dropbox and Github

  • Not compatible in general
  • Main computer: sync everything
  • Sub computer: sync only gitignored folders
  • Make sure to update gitignore when you re-sync and re-initialize the git
  • Make sure not to delete online smart-sync files
  • Move some files if necessary. Some files might not be synced from the remote github repo because they are ignored

When migrating the main computer

  • This method should work
    1. Make sure that the Dropbox is perfectly synced
    2. Check remote with git remote -v
    3. You don't need git init
  • (old) When there is huge, smart-synced files
    1. Make sure that every update is already available in the online repo
    2. Delete non-gitignored folders
    3. Re-clone the github repo to non-Dropbox folder
    4. Move files in the cloned folder to the existing corresponding folder in Dropbox
    5. Re-init as github repo
  • (old) When there is no smart-synced files
    1. Make sure that every update is already available in the online repo
    2. Move gitignored folders file to non-Dropbox folder
    3. Delete the github Dropbox folder
    4. Re-clone the github repo to Dropbox
    5. Put back files moved in Step 2 to the github repo

Install Obsidian

  • Setup Git and Github

Install Java

  • Java is required for some packages:
    • Python tabula-py
    • R tabulizer
$ brew install java
$ java --version

If java --version does not show the Java version, create a symlink for the system Java wrappers to find this JDK link

$ sudo ln -sfn /usr/local/Cellar/openjdk/18.0.2.1/libexec/openjdk.jdk \ /Library/Java/JavaVirtualMachines/openjdk.jdk

Accounts attached to mit address

  • notion
  • Slack
  • Zoom
  • Github
  • Spotify

Setup a mobile phone

Obsidian

Use Obsidian with Git

  • Follow the instruction here
    • Make sure to use the token in the password form
  • Once you finish authentication, specify the author name and email for commit in the setting of the plugin