Demo

UW Geospatial Data Analysis
CEE467/CEWA567
David Shean

Preparation and discussion

• Make sure all students are on Jupyterhub (add UW netid from Hub Control Panel if necessary)

• Distribute link to course Jupyterhub, have students start server

• Basic interface overview - start a shell, start a notebook (next week)

• Ask about OS? Anybody using Linux? All of you!

• Discuss virtual machine and cloud computing

  • underlying infrastructure, computer somewhere in Google data center in CA or OR

  • uname -a, lscpu, free, top, df -h .

• Close tab in Jupyterlab - demonstrate persistence

• Storage will persist throughout quarter, server will shut down after ~1 hour of inactivity

Shell overview

• Discussion of prompt (jovyan)

• Disucssion of file system navigation (all the way to /)

• Commands and arguments

• Tab completion

• ls -l - modificaiton timestamps

Set up git on Jupyterhub

• https://uwgda-jupyterbook.readthedocs.io/en/latest/resources/github.html#first-time-login

• Set up token

Basic git/Github workflow

1. Distribute Week 01 Github classroom assignment link through Slack channel

2. Clone assignment locally:

   git clone https://github.com/UW-GDA/01-shell-github-dshean.git
   cd gda_test  
   ls -l
   

3. git vs. github, local vs remote

4. Discuss repo contents - markdown files, csv

5. Pick a text editor

   • Demonstration of Jupyterlab text editor

   • Discuss text editors, pick one for command line

   • https://web.stanford.edu/class/cs107/resources/editors

6. Edit README.md and add your name

7. Commit the change

git status
git add README.md
git status
git commit -m "Added my name to README.md"
git status

Discussion of local vs origin

• Open web browser to view origin repo on Github

• git push

• Refresh page, verify README.md was updated

Edit README.md on Github, commit directly

• Add today’s date below your name

Pull changes to local repo

• git pull

• git log

Add a new file to the repo

Create a new text file

• nano git_reflections.txt

• Add some text “Git is …”

• Follow above add, commit, push

  • For now, always specify each file to commit

  • For now, modify single file, add and commit

  • Try without -m and demonstrate nano (how to get out)

Create a new text file

• Discuss extensions (.sh vs. .txt or .py)

• vim myawesomescript.py

• Add some lines:

  #! /usr/bin/env python
  print("Pancakes rule!")
  

Commit the change

git status
git add myawesomescript.py
git status
git commit -m "Added myawesomescript.py"

Try to execute script, doesn’t work

./myawesomescript.py

Check permissions

ls -l ./myawesomescript.py

Change permissions

chmod +x myawesomescript.py
ls -l myawesomescript.py
./myawesomescript.py

Commit permission change

git status
git diff myawesomescript.py
git add myawesomescript.py
git status
git commit -m "Change permissions on myawesomescript.py"

Review log, main is ahead of origin

git log
git log --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit

Push to origin

git push
git status

Review log, both origin and main are same

git log --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit

Other topics to discuss

• You will make mistakes, it’s OK, can always start over with git

• Post to #01_shell_github channel for help

• Best practices with git

  • https://stackoverflow.com/questions/572549/difference-between-git-add-a-and-git-add

  • https://uwgda-jupyterbook.readthedocs.io/en/latest/resources/github.html#why-are-a-bunch-of-random-files-added-to-my-repo

• Tab completion

• Command history (use up arrow)

• du and df

• top and ps

• ssh and scp

• tmux and screen

• Discuss filesystem

  • Output from which ls

  • Go to /

  • Explore /bin

• Discuss executables

• $PATH

• bits, bytes

• for loop

  for i in solutions.txt words README.md
  do
      ls $i
  done
  #One line:
  for i in solutions.txt words README.md; do ls $i; done
  

Introduce assignment

• create labs folder!

• Walk through first few questions of assignment together