Skip to content

Latest commit

 

History

History
238 lines (176 loc) · 8.44 KB

lab03-command-line-basics.md

File metadata and controls

238 lines (176 loc) · 8.44 KB
Raw

Lab 3: Command Line Basics and Git

Gaston Sanchez

Learning Objectives

  • Practicing with the command line
  • Navigating the filesystem and managing files
  • Practice basic manipulation of data files

Basic Bash shell commands

The first part of the lab involves navigating the file system and manipulating files (and directories) with the following basic bash commands:

  • pwd: print working directory
  • ls: list files and directories
  • cd: change directory (move to another directory)
  • mkdir: create a new directory
  • touch: create a new (empty) file
  • cp: copy file(s)
  • mv: rename file(s)
  • rm: delete file(s)

If you are using git-bash (i.e. your OS is Windows) you don't have the man command to see the manual documentation of other commands. In this case you can check the man pages online:

http://man7.org/linux/man-pages/index.html

Your turn

Write your bash commands in a text editor (NOT a word processor) and save them in a text file: e.g. lab03-gaston-sanchez.txt.

  • Open (or launch) the command line

  • Use mkdir to create a new directory stat133-lab03

  • Change to the directory stat133-lab03

  • Use the command curl to download the following text file:

    # the option is the letter O (Not the number 0)
curl -O http://textfiles.com/food/bread.txt

  • Use the command ls to list the contents in your current directory

  • Use the command curl to download these other text files:

  • Use the command curl to download the following csv files:

  • Now try ls -l to list the contents in your current directory in long format

  • Look at the man documentation of ls to find out how to list the contents in reverse order

  • How would you list the contents in long format and by time?

  • Inside stat133-lab03 create a directory data

  • Change to the directory data

  • Create a directory txt-files

  • Create a directory csv-files

  • Use the command mv to move the bread.txt file to the folder txt-files

  • Use the wildcard * to move all the text files to the directory txt-files

  • Use the wildcard * to move all the .csv files to the directory csv-files

  • Go back to the parent directory stat133-lab03

  • Create a directory copies

  • Use the command cp to copy the bread.txt file (the one inside the folder txt-files) to the copies directory

  • Use the wildcard * to copy all the .txt files in the directory copies

  • Use the wildcard * to copy all the .csv files in the directory copies

  • Change to the directory copies

  • Use the command mv to rename the file bread.txt as bread-recipe.txt

  • Rename the file Fisher.csv as iris.csv

  • Rename the file btaco.txt as breakfast-taco.txt

  • Change to the parent directory (i.e. stat133-lab03)

  • Rename the directory copies as copy-files

  • Find out how to use the rm command to delete the directory copy-files

  • List the contents of the directory txt-files displaying the results in reverse (alphabetical) order

Optional challenge

If you are already familiar with the basic bash commands to navigate the filesystem (or if you want to expand your R skills), use the R functions to manipulate files and directories to perform the exact same tasks from within R. See ?files for more information.

  • getwd()
  • setwd()
  • download.file()
  • dir.create()
  • list.files()
  • list.dirs()
  • file.create()
  • file.copy()
  • file.rename()
  • file.remove()

Git and GitHub Practice

Learning Objectives

  • Create a GitHub repository
  • Create a local Git repository
  • Practice adding, and committing changes to your (local) Git repo
  • Practice pushing commited changes to a remote repo

1) Create a New GitHub Repository

  • Open your browser and Sign in to your github account.
  • Locate the + button (next to your avatar).
  • Select the New repository option.
  • Choose a name for your repository: e.g. demo-repo.
  • In the Description field add a brief description: e.g. "this is a demo repo"
  • Use the default settings, and click the green button Create repository.
  • You should see some content similar (but not identical) to the one below:
echo "# Demo Repo" >> README.md
git init
git add README.md
git commit -m "first commit"
git remote add origin https://github.com/gastonstat/demo-repo.git
git push -u origin master

2) Create a local Git Repository

  • Open the terminal (Mac Terminal, or Git-Bash for Windows users).

  • Optional: change directory to your preferred location e.g. your Desktop

    cd Desktop

  • Create a directory with the name of your github repo

    mkdir demo-repo

  • Change to the directory you just created

    cd demo-repo

  • Initialize the directory as a git repository

    git init

It's possible that you encounter some error message, e.g. Mac users may get a message related with a missing component for CommandLineTools. If this your case, then type in the terminal console:

# Mac users may need to run this command
xcode-select --install

The command git init will set-up your directory demo-repo as a Git repository (NOT to confuse with your GitHub repository). This is basically your local repository.

3) Adding a README file

  • It is customary to add a README.md file at the top level. This file must contain (at least) a description of what the repository is about. The following command will create a README.md file with some minimalist content:

    echo "# Demo Repo" >> README.md

  • So far there you have a "new" file in your local repo, but this change has not been recorded by Git. You can confirm this by checking the status of the repo:

    git status

  • Notice that Git knows that README.md is untracked. So let's add the changes to Git's database:

    git add README.md

  • Check the status of the repo again:

    git status

  • Now Git is tracking the file README.md.

  • Next thing consists of committing the changes

    git commit -m "first commit"

4) Adding a remote

Right now you have a (local) Git repository in your computer. And you also have a GitHub repository in your GitHub account. Both repositories should have the same name, and the goal is to link them. To do this, you need to tell Git that a remote repository (i.e. the one in GitHub) will be added:

  • To add a remote repository use the command below with your own username:

    git remote add origin https://github.com/username/demo-repo.git

  • Verify your new remote

    git remote -v

  • If everything is okay, you should be able to see a message (with your own username) like this:

    # Verify new remote
origin  https://github.com/username/demo-repo.git (fetch)
origin  https://github.com/username/demo-repo.git (push)

5) Pushing changes to a remote repo

  • Now that you have linked your local repo with your remote repo, you can start pushing (i.e. uploading) commits to GitHub.

  • As part of the basic workflow with git and github, you want to constantly check the status of your repo

    git status

  • Now let's push your recent commit to the remote branch (origin) from the local branch (master):

    git push origin master

  • Go to your Github repository and refresh the browser. If everything went fine, you should be able to see the contents of your customized README.md file.

GitHub Classroom Repository

Read and follow the instructions to get your own GitHub Classroom repository, available in the following link:

lab03-github-classroom.pdf