The command line shell and git

• The default shell on OSX is bash, which is taught in this set of lessons: https://swcarpentry.github.io/shell-novice/ or in this detailed bash reference

• if you are on Windows, powershell is somewhat similar – here is a table listing commands for both shell side by side taken from this in-depth powershell tutorial

Using the command line

Powershell and Bash common commands

• To go to your $HOME folder:

cd ~

or

cd $HOME

• To open explorer or finder for the current folder:

windows explorer do:

   start .

MacOs finder do:

   open .

• To move up one folder:

cd ..

• To save typing, remember that hitting the tab key completes filenames

To configure powershell on windows

• first start a powershell terminal with admin privileges, then type:

  set-executionpolicy remotesigned

• then, in your miniconda3 powershel profile, do:

  Test-Path $profile

  to see whether you have an existing profile.

• if you don’t have a profile, then do the following (this will overwrite an existing profile, so be aware):

  New-Item –Path $Profile –Type File –Force

• To add to your profile, open with:

  start $profile

To configure bash or zsh on MacOS

• open a terminal then type either

  open .bash_profile

  or for Catalina

  open .zshenv

Bash and powershell command reference

Cmdlet	Alias	Bash Equivalent	Description
Get-ChildItem	gci	ls	List the directories and files in the current location.
Set-Location	sl	cd	Change to the directory at the given path. Typing .. rather than a path will move up one directory.
Push-Location	pushd	pushd	Changes to the directory.
Pop-Location	popd	popd	Changes back to the previous directory after using pushd
New-Item	ni	(touch)	Creates a new item. Used with no parameter, the item is by default a file. Using mkdir is a shortcut for including the parameter -ItemType dir.
mkdir	none	mkdir	Creates a new directory. (See New-Item.)
Explorer	start .	open .)	Open something using File Explorer (the GUI)
Remove-Item	rm	rm	Deletes something. Permanently!
Move-Item	mv	mv	Moves something. Takes two arguments - first a filename (i.e. its present path), then a path for its new location (including the name it should have there). By not changing the path, it can be used to rename files.
Copy-Item	cp	cp	Copies a file to a new location. Takes same arguments as move, but keeps the original file in its location.
Write-Output	write	echo	Outputs whatever you type. Use redirection to output to a file. Redirection with >> will add to the file, rather than overwriting contents.
Get-Content	gc	cat	Gets the contents of a file and prints it to the screen. Adding the parameter -TotalCount followed by a number x prints only the first x lines. Adding the parameter -Tail followed by a number x prints only the final x lines.
Select-String	sls	(grep)	Searches for specific content.
Measure-Object	measure	(wc)	Gets statistical information about an object. Use Get-Content and pipe the output to Measure-Object with the parameters -line, -word, and -character to get word count information.
>	none	>	Redirection. Puts the output of the command to the left of > into a file to the right of >.
\|	none	\|	Piping. Takes the output of the command to the left and uses it as the input for the command to the right.
Get-Help	none	man	Gets the help file for a cmdlet. Adding the parameter -online opens the help page on TechNet.
exit	none	exit	Exits PowerShell

Remember the keyboard shortcuts of tab for auto-completion and the up and down arrows to scroll through recent commands. These shortcuts can save a lot of typing!

Git

• A good place to go to learn git fundamentals is this lesson https://swcarpentry.github.io/git-novice/

Pulling changes from the github repository

When we commit changes to the master branch and push to our github repository, you’ll need to fetch those changes to keep current. To do that:

1. go to your fork of the repository on github. You should see a statement like “This branch is 1 commit ahead, 2 commits behind rwhite:main”.

2. click ‘Fetch upstream’ beside that statement and “Fetch and merge”. Now the statement should be something like “This branch is 2 commits ahead of rhwhite:main”

3. pull the changes into your own computer space. Make sure you aren’t going to clobber any of your own files:

   git status
   

   you can ignore “untracked files”, but pay attention to any files labeled “modified”. Those will be overwritten when you reset to our commit, so copy them to a new name or folder.

4. Get the new commit with

   git pull
   

Books and tutorials

• We will be referring to Phil Austin’s version of David Pine’s Introduction to Python: http://phaustin.github.io/pyman. The notebooks for each chapter are included in the numeric_students/pyman folder.

• If you are new to python, I would recommend you also go over the following short ebook in detail:

  • Jake Vanderplas’ Whirlwind tour of Python is available both as a set of notebooks which you can clone from github or as a free ebook: http://www.oreilly.com/programming/free/a-whirlwind-tour-of-python.csp

    • to get the notebooks do:

      git clone https://github.com/jakevdp/WhirlwindTourOfPython

• We will be referencing chapters from:

  • A Springer ebook from the UBC library: Numerical Python

    • with code on github:

      git clone https://github.com/jrjohansson/numerical-python-book-code

• Two other texts that are available as a set of notebooks you can clone with git:

  • https://github.com/fangohr/introduction-to-python-for-computational-science-and-engineering

  • https://github.com/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.ipynb

• My favorite O’Reilly book is:

  • Python for Data Analysis

• Some other resources:

  • If you know Matlab, there is Numpy for Maltab users

  • Here is a python translation by Don MacMillen of Chapter 1 of his matlab guide

  • Numpy beginners guide

  • Learning Ipython

  • The official Python tutorial

  • Numpy cookbook

  • A general computing introduction: How to think like a computer scientist with an interactive version

  • Think Stats

  • Think Bayes