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Which shell I am using?

Starting with macOS Catalina (10.15), Apple set the default shell to the Z shell (zsh). In previous macOS versions, the default was Bash.

  • In zsh, the configuration file is ~/.zshrc.

  • In bash, it’s ~/.bash_profile.

Every time you make changes with the configuration file, run the following command for the changes to take effect:

  • source ~/.bash_profile if you have bash.

  • source ~/.zshrc if the shell is zsh.

You can also type in any terminal you have opened:

$ echo $0
-zsh

The name of the shell will apear.

Or you could run

$ echo $SHELL
/bin/zsh

Relative Path

  • a dot (.) represents the current directory
  • a double dots (..) represents the parent directory

Get help

man cmd get manual page for cmd. E.g., man ls will display detailed info about the ls cmd, including its usage, options, and examples.

Once you’ve accessed a manual page, you can navigate through it using various commands. The common navigation keys include:

  • Spacebar: Move forward one page.
  • Enter: Move forward one line.
  • B: Move backward one page.
  • Q: Quit the manual viewer.

Linux man pages online: https://man7.org/linux/man-pages/index.html

You can search cmds online using the following search box.

Linux Manual Online

Apple bash commands: https://ss64.com/mac/

Q: What is CLT?
A: Common Line Tools.

Error: Cannot find man command.

Error Message looks like:

This system has been minimized by removing packages and content that are not required on a system that users do not log into.

To restore this content, including manpages, you can run the ‘unminimize’ command. You will still need to ensure the ‘man-db’ package is installed.

Cause: Typically man pages for Ubuntu commands not installed on a minimal cloud server or container-based images. To save hard disk space and to keep container image rebuild time smaller, man pages not installed.

Fix: install man pages.

Steps:

  1. Run the following commands as the root user using the sudo command or su command.

    sudo -i
## OR ##
su -

    Now you become the root.

  2. Search for Ubuntu man pages

    # search
apt search manpages
# see what the page does
apt info man-db

  3. Install man pages on server

    First update package index and then install manpages-posix package for all missing commands:

    sudo apt update
sudo apt install man-db manpages-posix

    Now you have installed man-db package.

  4. Install man pages for software development

    sudo apt install manpages-dev manpages-posix-dev

  5. Then run unminimize. That may takes a while.

    Now you can run man ls to check the syntax for ls command.

Reference: https://www.cyberciti.biz/faq/how-to-add-install-man-pages-on-ubuntu-linux/

which [flags] program locate a program file executed by the shell.

  • -a List all instances of executables found (instead of just the first one of each).

Specify flags/options for cmds: use a single dash (-) or a double dash (--).

  • - can be followed by any number of single-character flags.

  • -- can be followed only by a single, multi-character option.

    Using - is more compact, but it gets even MORE compact when you want to specify multiple flags.

    Consider:

    $ ls -l --size --human-readable --group-directories-first
$ ls -lshg

    While the two commands listed above are identical, the second one is clearly much quicker to type. If you use the wrong type of hyphen, for example specifying ls -size instead of ls --size, would be interpreted by the shell as equivalent to ls -s -i -z -e. As it happens, the -s options is the same as --size, but because there are no z or e options for the ls command, they are simply ignored.

` printenv` prints all environment variables.

ps stands for “process status.” It displays information about a list of active processes.

If ps is run with no argument, it will print all processes which were started from the current shell. Other processes will not be shown in this case.

Linux ps command

It displays the process ID (pid=PID), the terminal associated with the process (tname=TTY), the cumulated CPU time in [DD-]hh:mm:ss format (time=TIME), and the executable name (ucmd=CMD). Output is unsorted by default.

ps -A will show all processes being run on the system.

echo displays a mesage on screen.

echo -e enables interpret backslash escapes

INPUT: echo "abc\n def \nghi" 
OUTPUT:abc\n def \nghi

INPUT: echo -e "abc\n def \nghi"
OUTPUT:abc
 def 
ghi
  • -n Displays the output while omitting the newline after it.
  • -E The default option. Disables the interpretation of escape characters.
  • -e Enables the interpretation of escape characters.

$PATH Variable

Viewing the $PATH

You can check the value of the $PATH variable with the echo command”

  • echo $PATH print $PATH environment variable.

  • echo -e ${PATH//:/\\n} print each directory in $PATH on its own line.

How the $PATH works

The $PATH variable enables the system to locate the necessary programs without needing the full path for execution.

  • When you type a command, the shell looks for executable files in the directories specified by your PATH.
    • The directories are recursive, meaning if the parent folder is included, every file/folder inside is also included.
    • The order stands for precedence.

  • It’s a list of directory paths, separated by colons (:).

    For example, a default $PATH looks like /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin.

    If you have installed Homebrew, the $PATH should contain /opt/homebrew/bin (for Apple Silicon, such as M1, M2, or M3 CPUs) or /usr/local/bin (for macOS Intel). It should be among the highest priority directories, in a left-most position.

  • If you try to run an executable file or command that isn’t in one of the directories in your path, you’ll receive an error that says the “Command not found”.

    This often happens for programs you have installed that are not basic shell commands.

    If you don’t set the Mac $PATH, you’ll need to specify the full path to an executable every time. This can be tedious and annoying, especially for commands you use frequently.

    For example, if you install have an executable file Kando in the /Applications/Kando.app/Contents/MacOS/ directory, you may add the path to the folder to $PATH, or else you will need to type /Applications/Kando.app/Contents/MacOS/Kando every time you want to run the program.

    • Remember you may not be the only one trying to run the Kando program:

    If the cowsayprogram is called by another program and the $PATH is not set, it won’t be found and the program will fail.

  • Many applications and scripts rely on the $PATH variable to find necessary dependencies. Without a properly set $PATH, these applications will fail.

    • When you install a software package, the instructions will often tell you to add a directory to the $PATH variable. Make sure you do NOT overlook the step to add the directory to the $PATH variable.

Default Mac $PATH

  • Directories named bin are for “binaries” or executable command line programs.

  • The sbin directories are for system management programs.

  • The bin and /usr/bin directories are for basic command line programs provided by Apple.

  • The /usr/local/bin is for user-installed executables.

Add a new directory to the PATH

Add the following line to the bottom of ~/.zprofile.

export PATH=/Users/menghan/anaconda3:$PATH

The new $PATH variable will be exported to the environment as a combination of the previous $PATH plus a new directory.

  • In the above case, the new directory comes first; it will take precedence over any directories present in the previous $PATH.

    Alternatively, the new directory can be appended to the end of the $PATH:

    export PATH="$PATH:/new/dir1:/dir2:/dir/path/no3"

  • A : colon character separates the new directory path from the existing directories in the previous $PATH.

Set the $PATH in script

There are a number of config files containing PATH information. The following are some examples:

System-wide:
/etc/paths

User-specific:

1) Bash:

~/.bash_profile
~/.bashrc

2) Zsh

~/.zprofile
~/.bashrc
~/.zshenv

Set the $PATH environment variable in the ~/.zprofile (Zsh Shell) or ~/.bash_profile (Bash Shell) file.

The tilde ~/ is a Unix abbreviation for your home directory. That is, the .zprofile file belongs in your home directory.

Zsh recognizes four different configuration files in the user’s home directory: ~/.zshenv, ~/.zprofile, ~/.zshrc, and ~/.zlogin. The article .zshrc or .zprofile explains the differences. Here is a summary:

  • ~/.zshrc (Zsh Run Control): This file is best for adjusting the appearance and behavior of the shell, such as setting command aliases and adjusting the shell prompt.

    • Loaded only for interactive shell sessions. It is loaded whenever you open a new terminal window or launch a subshell from a terminal window.

    • This is the configuration file that most developers use.

      Use it to set aliases and a custom prompt for the terminal window. By convention and design, ~/.zshrc is intended for customizing the look and feel of the interactive terminal.

      You can also use it to set the PATH (which many people do) but ~/.zprofile is preferred.

  • ~/.zprofile (Zsh Profile): This file is ideal for commands that should be executed only when the terminal window is opened, such as setting the $PATH environment variable.

    • Loaded for login shells (both interactive and the rare non-interactive sessions).

    • Homebrew recommends setting the PATH variable here.

      There’s a reason PATH should be set in ~/.zprofile and not the universal ~/.zshenvfile: the macOS runs a utility path_helper(from /etc/zprofile) that sets the PATH order before ~/.zprofileis loaded.

    • MacOS uses this to set up the shell for any new terminal window. Subshells that start within the terminal window inherit settings but don’t load ~/.zprofile again.

  • ~/.zshenv This is loaded universally for all types of shell sessions (interactive or non-interactive, login or non-login).

    • It is the only configuration file that gets loaded for non-interactive and non-login scripts for automated processes like cron jobs. However, macOS overrides this for PATHsettings for interactive shells.
    • As a beginner, you will not use this configuration file. In fact, few experienced macOS developers use it.

  • ~/.zlogin Only used for login shell configurations, loaded after .zprofile. This is loaded whenever you open a new terminal window.

By default, the ~/.zprofile and ~/.zshrc configuration files do NOT exist for a user on a new Mac. You’ll need to manually create the file in your home directory to properly configure your development environment.

You can create a new file from the command line with the touch command:

$ touch ~/.zprofile

After you create the file, you can edit it.

You can use TextEdit, the default macOS graphical text editor, to edit the shell configuration files. You can open a file in TextEdit from the Mac Terminal:

$ open -e ~/.zprofile

You also can use the command line editors nano or vim to edit the shell configuration files. See Shell Configuration for more about editing shell configuration files.

For the changes in ~/.zprofile to take effect, you have to log out and log in again.

Alternatively, to apply the changes immediately in an existing session, you can source:

$ source ~/.zprofile

The source command reads and executes a shell script file, in this case resetting the shell environment with your new $PATH setting.

Finally, you can verify the new path settings

$ echo $PATH

Reference: https://mac.install.guide/terminal/path

Install tar.gz on macOS

  1. Finder

    https://stackoverflow.com/questions/62988753/install-tar-gz-on-mac

    1. Double click the tar.gz file to open it

    2. One of the new files might be a unix executable that looks like this:

      Executable

  2. Command line

    Download the desired .tar.gz or (.tar.bz2) file. Open Terminal, extract the .tar.gz or (.tar.bz2) file with the following commands:

    tar xvzf PACKAGENAME.tar.gz 
tar xvjf PACKAGENAME.tar.bz2

    Navigate to the extracted folder using cd command

    cd PACKAGENAME

    Now run the following command to install the tarball

     ./configure 
 make 
 sudo make install

​

tar [options] [archive-file] [file or directory to be archived] options:

  • x extract the archive;
  • v print its action on console;
  • f tell tar which file to perform the action on;
  • z compress the tar file using gzip
  • j compress the tar file using bzip2

tar xvjf PACKAGENAME.tar.gz -C / -C means changing directory.

man tar to show help page for tar.

echo $PATH check $PATH variable.

  • stored in ~/.bash_profile.

  • in R

    Sys.getenv("PATH")

touch ~/.R/Makevars create a file ~/.R/Makevars

source $SHELL restart your session to enable new settings.

File Management

cp [option] <source> <destination> copy the <source> file to the <destination> file or directory. If multiple <source> is provided, then copy all files to the <destination> directory. Options:

  • -i interactive copying. Warn the user before overwriting the desitnation file.
  • -r or -R recursive copying the entire directory structure.

rm DeleteMe.odt DeleteMe2.odt delete multiple files.

  • If there are special characters in file names, simply add quotes to file names. E.g.,

    rm '4-way mini-roundabout.png' 'DTC.png' 'Heyford.png' 'image-20220824132439609.png' 'image-20220824133418559.png'

  • If the file doesn’t exit, there will be warning message No such file or directory.

# R codes to generate the shell cmd to delete files

# delete repetitive files
post_image <- list.files("~/Documents/PhD Courses/Econ-Study/images")
post_image

google_drive <- list.files("~/Library/CloudStorage/GoogleDrive-my1396@nyu.edu/My Drive/Typora_images")
google_drive

mask <- google_drive %in% post_image
google_drive[!mask]

file_delete <- google_drive[mask]
file_delete <- as_tibble_col(file_delete, column_name = "name")
# add quotes to file names to escape special characters
file_delete <- file_delete %>% 
  mutate(new_name = paste0("'", name, "'") 
  )
file_delete
nrow(file_delete)

# cmd to delete files
paste0("rm ", paste(file_delete$new_name[1:5], collapse = " "))

length(google_drive)
length(post_image)
length(list.files("~/Library/CloudStorage/GoogleDrive-my1396@nyu.edu/My Drive/Typora_images"))

Hardlink vs symbolic link

  • Once a hard link has been made the link is to the inode. Deleting, renaming, or moving the original file will not affect the hard link as it links to the underlying inode. Any changes to the data on the inode is reflected in all files that refer to that inode.

  • Hardlinks can only refer to files within the same volume otherwise symbolic links will be needed.

  • Symbolic links point to the original file, changing the symboliclink should change the original file.

    What will break a symbolic link is when the original file is moved to a different file or deleted.

    ln original_file link_file # hardlink
ln -s original_file link_file # softlink (more felxible)
ln –s /Users/admin/Documents /Users/admin/Desktop # create a symbolic link for my Documents folder on the Desktop
rm /Users/admin/Desktop/Documents # remove symbolic link

And to check the current status of the service, you’d have to use the systemctl command in the following manner:

systemctl status <service-name>

Understanding systemctl states:

  • active (running): Service is actively running in the background.
  • active (exited): Indicates the service was meant to be executed one time or periodically. So the service did its job and then exit upon completion.

  • active (waiting): It indicates the service is running but it is waiting to be triggered by some condition like a specific event.

  • inactive: Service is not currently running.

  • enabled: Service will be enabled at system boot time.

  • disabled: Service is disabled and won’t be started at system boot.

  • static: It means the specific service can’t be managed using systemd (or the systemctl command) and you’d need to have another init service or manage it manually.

  • masked: This means the service is masked and can’t be stated directly using the systemctl command. This can be helpful when you want to prevent accidental starting of service.

  • alias: It indicates the service name is an alias and the service is a symlink pointing to another unit file.

  • linked: It indicates that the service or the unit file is symbolically linked to another unit file.

open will open files and directories, just as if you had double-clicked the file’s icon.

  • -a open an application.
  • -n Open a new instance of the application(s) even if one is already running
# open a new instance of RStudio, useful for coding in multiple sessions
open -n /Applications/RStudio.app

# open URL with specified browswer
open -a "Google Chrome" "https://stackoverflow.com"