computer_basics.md

Setting Up a Computer Environment for Research

Terminal Tools

Terminal Emulator

• iTerm2 - macOS Terminal Replacement

  • A nice free choice for MacOSX. iTerm2 brings the terminal into the modern age with features you never knew you always wanted.
  • A cheat sheet of iTerm2 shortcuts

• It becomes easier and easier to do research under Windows system:

  • Microsoft's terminal - The new Windows Terminal, and the original Windows console host
  • cmder - Portable console emulator for Windows

• Different Linux releases have there own default terminal emulator and normally they are good enough for research works. Meanwhile, there are some nice choices of drop-down style emulators:

  • tilda - A Gtk based drop down terminal for Linux and Unix
  • guake - Drop-down terminal for GNOME
    • Guake is a dropdown terminal made for the GNOME desktop environment. Guake's style of window is based on an FPS game, and one of its goals is to be easy to reach.

Terminal Multiplexer

• GNU Screen

  • Screen is available in most Unix/Linux system release.
  • How to use Linux Screen

• tmux - a terminal multiplexer for Unix-like operating systems

  • Similar to Screen. There are a lot of discussions about the pros and cons of Screen and tmux, but as a beginner, either is fine.
  • Read A tmux crash course and tmux shortcuts and cheat sheet before you use it.

Shell Environment

Fluency on the command line is a skill often neglected or considered arcane, but it improves your flexibility and productivity as an engineer in both obvious and subtle ways. -- The Art of Command Line

• The same also applies to student of science and researcher.

• The Art of Command Line

  • In multiple languages, including Chinese

• 37 Important Linux Commands You Should Know

• awesome-command-line-apps - Use your terminal shell to do awesome things

  • A curated list of useful command line apps, in celebration of the TUI.

• awesome-macos-command-line - Use your macOS terminal shell to do awesome things

  • A curated list of shell commands and tools specific to OS X.
  • A lot of these actually work for Linux too.

Regular Expression

• Regular expression (regex) is a group of characters or symbols which is used to find a specific pattern from a text. It is very useful to learn the basic of regex.

• Learn Regex the Easy Way

  • There is a Chinese version

Bash related

• Pure Bash Bible

  • A collection of pure bash alternatives to external processes.

• Bash Notebook

  • In depth Bash notebook in multiple languages

• Bash-it - a collection of community Bash commands and scripts for Bash 3.2+

  • Achieve some of zsh's functions in bash.

Other than bash

• Oh My Zsh

  • Code on Github is here

• The Fish Cookbook

  • Tips and recipes for fish, from shell to plate

Version Control

Git

• git is the most widely used software for version control and it is extremely useful to learn the basic of it.

  • Plenty of reference and examples are provided in the above webpage including many short videos.

• Learn Git with Bitbucket Cloud is another good place to start learning about version control using git.

  • Git cheat sheet and Advanced Git Tutorials.

• Oh shit, git!

  • A very practical guide for when you screw up in git.

Others

• mercurial is another popular version control software.

System Tools

• gotop - system monitor

  • A terminal based graphical activity monitor inspired by gtop and vtop

• tldr - command document for human

  • Simplified and community-driven man pages

• thefuck - Magnificent app which corrects your previous console command

  • Well....it is actually kind of useful...

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MacOS

• mac-setup: Installing Development environment on macOS
  • The more readable website is here

Mount harddrive in Linux file system

• Linux system uses ext4 or other similar file system that is not automatically readable under MacOSX. The ext4fuse software will be useful.

  • Please read this stackexchange thread for more details.

• ExtFS is not a free software. It costs you $39.95 but it is claimed to be able to mount or even repair ext system under MacOSX