Setting Up a Computer Environment for Research
==============================================

Terminal Tools
--------------

Terminal Emulator
~~~~~~~~~~~~~~~~~

-  `iTerm2 - macOS Terminal Replacement <https://www.iterm2.com/>`__

   -  A nice free choice for **MacOSX**.
      `iTerm2 <https://github.com/gnachman/iTerm2>`__ brings the
      terminal into the modern age with features you never knew you
      always wanted.
   -  A `cheat sheet of iTerm2
      shortcuts <https://gist.github.com/squarism/ae3613daf5c01a98ba3a>`__

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

   -  `Microsoft’s terminal - The new Windows Terminal, and the original
      Windows console host <https://github.com/microsoft/terminal>`__
   -  `cmder - Portable console emulator for
      Windows <https://cmder.net/>`__

-  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 <https://github.com/lanoxx/tilda>`__
   -  `guake - Drop-down terminal for
      GNOME <https://github.com/Guake/guake>`__

      -  **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 <http://git.savannah.gnu.org/cgit/screen.git>`__

   -  **Screen** is available in most Unix/Linux system release.
   -  `How to use Linux
      Screen <https://linuxize.com/post/how-to-use-linux-screen/>`__

-  `tmux - a terminal multiplexer for Unix-like operating
   systems <https://github.com/tmux/tmux>`__

   -  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 <https://thoughtbot.com/blog/a-tmux-crash-course>`__ and
      `tmux shortcuts and cheat
      sheet <https://gist.github.com/MohamedAlaa/2961058>`__ 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 <https://github.com/jlevy/the-art-of-command-line>`__

   -  In multiple languages, including Chinese

-  `37 Important Linux Commands You Should
   Know <https://www.howtogeek.com/412055/37-important-linux-commands-you-should-know/>`__

-  `awesome-command-line-apps - Use your terminal shell to do awesome
   things <https://github.com/herrbischoff/awesome-command-line-apps>`__

   -  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 <https://github.com/herrbischoff/awesome-macos-command-line>`__

   -  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 <https://github.com/ziishaned/learn-regex>`__

   -  There is a `Chinese
      version <https://github.com/ziishaned/learn-regex/blob/master/translations/README-cn.md>`__

**Bash** related
~~~~~~~~~~~~~~~~

-  `Pure Bash Bible <https://github.com/dylanaraps/pure-bash-bible>`__

   -  A collection of pure bash alternatives to external processes.

-  `Bash Notebook <https://github.com/denysdovhan/bash-handbook>`__

   -  In depth Bash notebook in multiple languages

-  `Bash-it - a collection of community Bash commands and scripts for
   Bash 3.2+ <https://github.com/Bash-it/bash-it>`__

   -  Achieve some of **zsh**\ ’s functions in **bash**.

Other than **bash**
~~~~~~~~~~~~~~~~~~~

-  `Oh My Zsh <https://ohmyz.sh/>`__

   -  Code on Github is
      `here <https://github.com/robbyrussell/oh-my-zsh/>`__

-  `The Fish Cookbook <https://github.com/jorgebucaran/fish-cookbook>`__

   -  Tips and recipes for fish, from shell to plate

Version Control
---------------

**Git**
~~~~~~~

-  `git <https://git-scm.com/doc>`__ 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 <https://www.atlassian.com/git/tutorials/learn-git-with-bitbucket-cloud>`__
   is another good place to start learning about version control using
   **git**.

   -  `Git cheat
      sheet <https://www.atlassian.com/git/tutorials/atlassian-git-cheatsheet>`__
      and `Advanced Git
      Tutorials <https://www.atlassian.com/git/tutorials/advanced-overview>`__.

-  `Oh shit, git! <http://ohshitgit.com/>`__

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

Others
~~~~~~

-  `mercurial <https://www.mercurial-scm.org/>`__ is another popular
   version control software.

System Tools
------------

-  `gotop - system monitor <https://github.com/cjbassi/gotop>`__

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

-  `tldr - command document for
   human <https://github.com/tldr-pages/tldr>`__

   -  Simplified and community-driven man pages

-  `thefuck - Magnificent app which corrects your previous console
   command <https://github.com/nvbn/thefuck>`__

   -  Well….it is actually kind of useful…

--------------

MacOS
-----

-  `mac-setup: Installing Development environment on
   macOS <https://github.com/sb2nov/mac-setup>`__

   -  The more readable website is
      `here <http://sourabhbajaj.com/mac-setup/iTerm/tree.html>`__

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 <https://github.com/gerard/ext4fuse>`__ will be useful.

   -  Please read `this stackexchange
      thread <https://apple.stackexchange.com/questions/210198/mount-ext4-on-el-capitan>`__
      for more details.

-  `ExtFS <https://www.paragon-software.com/us/home/extfs-mac/>`__ 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**