This post contains details of how I set up my shell and environment. I use Windows, Mac, and Linux on a daily basis, so I have different setups for different purposes, but I try to make them similar when I can. You can see the softwhere I use and how I customize it in the linked posts; this post will focus on setup.

Table of Contents

Shell
- Shell Configuration
  - Development Environment
Installing Homebrew
Aliasing
- Additions to Other Files
Packages
Exports
Aliases
Functions
Shell-specific
- ZSH
My .zshrc
Working on Remote Linux Instances
- Adding credentials to .my_credentials
Bash
Alias Notes
Finding How Things Got in Environment
Useful Git Commands
Old
- Exports

Shell

On Macs, I use zsh as my main shell. It’s the default shell now but older Macs will need to install it. My setup is based around zsh.

Shell Configuration

I use Oh My Zsh to configure zsh and highly recommend it.

Development Environment

I have a particular way I set up my development environment. I store all of my aliases and environment variables other than my passwords in a ~/.profile file. This way I can share it with a team and we can all have the same hotkeys. In ~/.profile, I source a separate file called something like .my_credentials, which is where all my credentials are exported from.

I source ~/.profile from whatever shell I’m using. If I’m using Oh My Zsh, I create a file that just says source ~/.profile and save it at ~/.oh-my-zsh/custom/profile.zsh. I usually leave the .zshrc file alone, but you can customize the Oh My Zsh theme if you want. Sometimes other applications, like Anaconda, will modify the .zshrc file. This is fine, but for everything I add, I put it in ~.profile.

The full chain looks like this:

~/.zshrc -> ~/.oh-my-zsh/custom/profile.zsh -> ~/.profile -> ~/.my_credentials

Also .profile will source .bash_profile if it exists

Installing Homebrew

Homebrew is the best package manager for Mac. It installs in /usr/local for macOS Intel and /opt/homebrew for Apple Silicon. You can run the right location either way with this:

# Set Homebrew path and run eval
HOMEBREW_PREFIX=$(brew --prefix)
if [[ -d "${HOMEBREW_PREFIX}" ]]; then
  eval "$("${HOMEBREW_PREFIX}/bin/brew" shellenv)"
fi

Aliasing

Additions to Other Files

Sometimes other applications will place information in your profile files. Some examples:

brew puts something in zprofile
conda adds to .zshrc or sometimes .bash_profile depending on how you install it.

Packages

There are a few packages I use to improve my terminal experience.

Pygments

Pygments, a Python syntax highlighter. It’s like cat with colors. I alias it to c (as seen below).

Autojump

autojump

ZSH Syntax Highlighting

zsh-syntax-highlighting

To activate the syntax highlighting, add the following at the end of your .zshrc: source /opt/homebrew/share/zsh-syntax-highlighting/zsh-syntax-highlighting.zsh

If you receive “highlighters directory not found” error message, you may need to add the following to your .zshenv: export ZSH_HIGHLIGHT_HIGHLIGHTERS_DIR=/opt/homebrew/share/zsh-syntax-highlighting/highlighters

Exports

export BASE="$HOME/git"
export DATA="$HOME/data"
export MODELS="$HOME/models"
export FZF_DEFAULT_OPS="--extended"

Aliases

# GENERAL ALIASES

## MOVING AROUND

alias cdh="cd $BASE"

alias please='sudo $(history -p !!)' # redo last command but with sudo
alias ff='find . -name' # find file
alias ftxt='grep -rnw . -e'
alias fpy='find . -name "*.py" | xargs grep --color'
alias grep='grep --color=auto'
alias hgrep='history | grep -v grep | grep '

alias ll='ls -GlAFh'
alias lls='ls -GlAFhS'


alias c='pygmentize -g' # like cat but with color
alias t='tail -v'

alias ckenv='printenv | grep -i' # check environmental variables
alias path='echo $PATH | tr ":" "\n"'
alias mkdir='mkdir -pv' # automatically make child directories


alias pu='popd'
alias pd='pushd'
alias c='clear'


## DATA SCIENCE

alias ip='ipython'
alias nb='jupyter notebook'
alias wgpu='watch -d -n 0.5 gpustat' # requires gpustat
alias ns='watch -d -n 0.5 $BASE/nvidia-htop.py'
alias catf='conda activate tf' # tensorflow environment
alias capt='conda activate pt' # pytorch environment


## TMUX ALIASES

alias tmn='tmux new-session'
alias tmk='tmux kill-session -t'
alias tma='tmux a -t'
alias tm='tmux ls'

## GIT ALIASES

alias gs='git status'

Functions

# find text
function ft {
  grep -rn . -e "$1"
}

function cheat() {
      curl cht.sh/$1
  }

function extract () {
      if [ -f $1 ] ; then
        case $1 in
          *.tar.bz2)   tar xjf $1     ;;
          *.tar.gz)    tar xzf $1     ;;
          *.bz2)       bunzip2 $1     ;;
          *.rar)       unrar e $1     ;;
          *.gz)        gunzip $1      ;;
          *.tar)       tar xf $1      ;;
          *.tbz2)      tar xjf $1     ;;
          *.tgz)       tar xzf $1     ;;
          *.zip)       unzip $1       ;;
          *.Z)         uncompress $1  ;;
          *.7z)        7z x $1        ;;
          *)     echo "'$1' cannot be extracted via extract()" ;;
           esac
       else
           echo "'$1' is not a valid file"
       fi
     }

Shell-specific

ZSH

   alias rld='source ~/.zshrc' #reload profile

  # zsh syntax highlighting
  source /usr/local/share/zsh-syntax-highlighting/zsh-syntax-highlighting.zsh

  ## allow autojump
  [ -f /usr/local/etc/profile.d/autojump.sh ] && . /usr/local/etc/profile.d/autojump.sh

  ## allow autojump - ubuntu
  [[ -s /home/julius/.autojump/etc/profile.d/autojump.sh ]] && source /home/julius/.autojump/etc/profile.d/autojump.sh

  autoload -U compinit && compinit -u

#### BASH
```bash
  # remote GPUs run bash
   alias rld='source ~/.bashrc' #reload profile

   [[ -s /usr/share/autojump/autojump.sh ]] && source /usr/share/autojump/autojump.sh

My .zshrc

Conda will install the initialization script for conda inside .zshrc (for Macs). It will depend on whether you installed Anaconda or Miniconda, and on whether you installed in for a single user or for all users. If it’s installed for all users it will be somewhere like /opt/anaconda3/etc/profile.d/conda.sh. If it’s just installed for one user it will be somewhere like /Users/$USER/opt/anaconda3/etc/profile.d/conda.sh. The whole initialization looks like one of the following (depending on whether you use Anaconda or Miniconda):

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/jsimonelli/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/jsimonelli/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/jsimonelli/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/julius/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/julius/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/julius/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/julius/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

It’s fine to keep in there, but if you use tmux, you might run into a problem. tmux doesn’t always source .zshrc. Sometimes it only sources .profile, so conda won’t load in a tmux window. Even worse, it may pull Python from /usr/bin/python, which will be old Python 2 (use which python to see which python is being used). So you might want to cut and paste the initialization over to .profile.

I have found that if I don’t include conda activate $DEFAULT_CONDA_ENVIRONMENT in my .zshrc, it doesn’t activate my default profile, even though I have this in my .profile. So I leave it in .zshrc.

Other stuff is added to .zshrc automatically as well. Things like [ -f ~/.fzf.zsh ] && source ~/.fzf.zsh automatically get added here. If you don’t need it for tmux, you can leave it here. Otherwise I would recommend moving it all over to .profile.

Working on Remote Linux Instances

If you’re sshing into a remote Linux machine, you may have to set things up differently.

You’re likely to have a .bashrc and that will have stuff like export PS1="\u@\h \[\e[32m\]\w \[\e[91m\]\$(parse_git_branch)\[\e[00m\]$ " in it. It will also have your conda init. You will also want to put you .my_credentials file there, and may need to add a export REMOTE_BASE="/home/me" there.

Adding credentials to `.my_credentials`

You might also want some environmental variables in your credentials file, especially if you are using it for other purposes. You can make it depend on the shell like so

export LOCAL_PATH="/Users/me"
export REMOTE_PATH="/home/me"

if [ -n "`$SHELL -c 'echo $ZSH_VERSION'`" ]; then
   # PUT YOUR LOCAL DATASET LOCATION HERE
  export TRUE_PATH=$LOCAL_PATH


elif [ -n "`$SHELL -c 'echo $BASH_VERSION'`" ]; then

  # remote GPUs run bash
   alias rld='source ~/.bashrc' #reload profile

   export TRUE_PATH=$REMOTE_PATH

else
   echo "Warning: Shell unknown"
fi

Bash

I still use Bash fairly often, and because it doesn’t come with all the same aliases that Oh My Zsh does, I have to add some of the most important ones manually. I use all the ones I use for zsh but I add these as well.

if [ $SHELL = "/bin/bash" ]
then
	shopt -s histappend                      # append to history, don't overwrite it
	bind '"\e[A":history-search-backward'
	bind '"\e[B":history-search-forward'
fi

alias ..='cd ..'
alias ...='cd ../../../'
alias ....='cd ../../../../'

conda activate "$DEFAULT_CONDA_ENVIRONMENT"
 
#color git branch:
parse_git_branch() {
     git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/(\1)/'
}
export PS1="\u@\h \[\e[32m\]\w \[\e[91m\]\$(parse_git_branch)\[\e[00m\]$ "


# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    #alias dir='dir --color=auto'
    #alias vdir='vdir --color=auto'

    alias grep='grep --color=auto'
    alias fgrep='fgrep --color=auto'
    alias egrep='egrep --color=auto'
fi

I also like to customize the git prompt if it’s not already done for me. Here’s one I like:

parse_git_branch() {
     git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/(\1)/'
}
# customize the zsh prompt
PS1='%B%F{green}%(?.%F{green}√.%F{red}X:%?) %B%F{251} %1~ $(parse_git_branch)\ %# '

Alias Notes

If you make a shortcut to your code base like so:

export BASE='$HOME/git'

then if you want to use it in an alias you’ll have to use double quotes.

Instead of alias cdh=cd $BASE' you’ll have to use alias cdh="cd $BASE"

However, if you were just doing it with $HOME, it seems single quotes work.

Finding How Things Got in Environment

If you want to find how something got in your conda environment, you could grep it like this:

grep 'how_did_this_get_here' ~/.bashrc ~/.bash_profile ~/.profile

Useful Git Commands

These are good to set to an alias

git log --pretty=format:'%C(yellow)%h %Cred%ad %Cblue%an%Cgreen%d %Creset%s' --date=short

Testing:

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color|*-256color) color_prompt=yes;;
esac

Old

Exports

export HISTSIZE=1000000
export HISTFILESIZE=1000000000
export HISTCONTROL=ignoredups:erasedups  # no duplicate entries

# general aliases


#redo last command but with sudo
alias psgrep='ps aux | grep -v grep | grep '


alias ccat='pygmentize -O style=monokai -f console256 -g'
alias c='pygmentize -g' # like cat but with color
alias pu='popd'
alias pd='pushd'
alias c='clear'
# See what's in your path


# Watch GPU usage
alias wgpu='watch -d -n 0.5 nvidia-smi'
alias ns='watch -d -n 0.5 $OI_BASE/core/nvidia-htop/nvidia-htop.py'
#alias wgpu='watch -d -n 0.5 gpustat' # requires gpustat
#alias ns='watch -d -n 0.5 nvidia-htop.py


# Moving around
alias cdh='cd ~/git'

# conda
alias catf='conda activate tf' # tensorflow environment
alias capt='conda activate pt' # pytorch environment

# git
alias gs='git status'

Julius' Data Science Blog

Linux Setup

Shell

Shell Configuration

Development Environment

Installing Homebrew

Aliasing

Additions to Other Files

Packages

Pygments

Autojump

ZSH Syntax Highlighting

Exports

Aliases

Functions

Shell-specific

ZSH

My .zshrc

Working on Remote Linux Instances

Adding credentials to `.my_credentials`

Bash

Alias Notes

Finding How Things Got in Environment

Useful Git Commands

Old

Exports

Shell

Shell Configuration

Development Environment

Installing Homebrew

Aliasing

Additions to Other Files

Packages

Pygments

Autojump

ZSH Syntax Highlighting

Exports

Aliases

Functions

Shell-specific

ZSH

My .zshrc

Working on Remote Linux Instances

Adding credentials to .my_credentials

Bash

Alias Notes

Finding How Things Got in Environment

Useful Git Commands

Old

Exports

Adding credentials to `.my_credentials`