The best way to directly interact with your computer is through the terminal window. This terminal (in Mac and Linux OSs) is the unix shell, and is commonly referred to as the bash shell, though bash is only one flavor of unix shell (e.g., Ksh shell, fish).
We will use the bash shell to run some of our programs, and help with makefiles and travis-CI builds, which we will go over at some point. On a basic level, the ability to us the bash shell is incredibly useful for copying/moving/deleting files (especially in bulk) and the automation of repetitive tasks.
Open up the terminal.
You should see, at least in Ubuntu, your username followed by a “@”
and the name of your machine (e.g., tad@poe), followed by
“:~$” and a blinking cursor. You are in the home directory by default.
To see this, issue the command
pwdwhich should output “/home/name”, where “name” is your username (again, this may be specific to Linux OSs).
To change the directory that you are in, you use the cd
command.
cd Documentsshould navigate you to the Documents folder (assuming that it
exists). To test if it exists, we can examine all the items in the
current directory by using the ls command.
ls -lHere, we issued the ls command with the -l
argument. Adding arguments to functions allows for customizable output.
Here, we ask ls to output additional information on modification date,
permissions, file size, etc. To see the other possible arguments we
could have given the function, we can use
ls --help
man lsThe --help argument should work with any shell based
command.
Directories are structured hierarchically, so
home/tad/Documents means that the Documents
folder is nested within the tad folder which is nested
within home. To back up levels, we can use relative paths.
For instance, if we wish to back up one level,
cd '..'or two levels
cd '../..'By default, if you issue cd without any arguments, you
will be returned to your home directory.
Another useful tool is the use of wildcards, which allow you to target certain files without knowing their exact name. For instance, if you want to list all files in the working directory that have a certain extension (e.g., ‘.txt’), you could issue the command
ls *.txtHere, the star means “anything” and the .txt constrains the ls to just .txt files.
A few other important functions are given below. The best way to learn about them is to read the –help file, and to play around with using them. I list the commands below, and then we can take some time to practice interacting with our machines through bash shell.
Do all of this from command line. 1. create a folder called “firstRepo” 2. navigate into the folder 3. create a file called “README.md” 4. use nano to write “This is my first GitHub repo”, save and exit.
This section will focus on how to install things on Ubuntu. If we want to install a program called htop, we could issue:
apt-get install htopHowever, this should error out and saying something like “Permission denied” and ask “are you root?”. You are not. Being “root” means you have permissions to install and modify all files. We will not go into permissions in much detail here. However, to get root access, you have to pre-empt the command by “sudo”, and you will be prompted for your password.
sudo apt-get install htop
sudo apt install htopYou also do not strictly need the “-get” part of that. This is a holdover from an earlier version, and I just stuck with it due to muscle memory.
Finally, this should rarely (fingers crossed) be the case when working on these lab computers for people in the course, as I requested that all (hopefully) necessary packages and such be installed prior to you sitting in that seat.
Now we will demonstrate how to use command line utilities. These are
things that do not have a GUI (graphical user interface), and therefore
must be run through the command line (e.g., nano). The thing we will
learn to use through command line is a version control software called
git.
Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later.
Version control is important both for collaborative coding with team members, and for developing your own code locally. Using version control software as an individual is important to have a constant backup of previously developed files, charting a clear timeline of progress on a particular project. Using version control software as a team helps keep every team member working off the latest version, or allows team members to develop add-ons without breaking the main flow of the code.
I want you to use the folder you made above called
firstRepo as your first GitHub repo. So navigate to it from
command line. Now, initiate the folder as a git repository (i.e.,
repo).
git initThis creates a .git folder which houses information on
each version of the repo. A quick aside that we will have to do is
git remote add origin '/path/to/your/folder'This part will become unnecessary when we interface with Github (discussed below), and is only needed when you are setting up a version controlled project that will only ever exist on your local machine. There are still numerous benefits to version controlling your work on your own machine, but the power of git goes well beyond this.
To properly version control, you have to take periodic “snapshots” of
the contents of the repo, tracking changes in files across time. To take
a “snapshot”, we have to do a “commit”. This is git jargon,
and I will go over it below, introducing all the terms at once to
hopefully provide a glossary and clear programmatic flow.
git add
git commit -m 'message'
git push origin masterSo all git commands start by using the prefix “git”, as above, into
the bash shell. The order of events is as such. First, we
add files to the commit, telling git which
files we want to include in the commit. Files that we do not include are
not removed, but they just are not versioned in that commit.
Next, we make a commit, and supply some informative
message about what was changed using the -m argument to the
commit function.
After this, we simply push the changes, which takes all the changes that were staged during the process of adding the files and then committing the files, and creates a clear record.
Github is an online hosting platform for your git repositories. That is, you can maintain a versioned history of your files independent of the internet and any potential collaborators, but by hosting on a platform like Github, you can collaboratively develop files with other people, and everything remains nicely versioned. This is important, as this will be how you turn in assignments. I expect that you will leave this class with a solid working knowledge of git and Github.
Go to https://github.com/ and set up your account if you have not already done so.
Recall when we added a remote to the local git repo? To
refresh your memory, we issued this command
git remote add origin '/path/to/your/folder'which was just a workaround that we probably did not even strictly
need. The reason why we did not need it is because remotes,
by definition, are for remote projects. That is, we use
remotes to manage projects that will be hosted on internet
services (like Github!). So now we will change the remote of this
project to point to Github. To do this, we first have to set up the
remote repo on Github.
To do this, we will navigate to our account on Github, and click the
+ dropdown menu in the top right corner, selecting “New
repository”. We fill out the relevant information, and create it. Then,
we can go back to our local repo, and set the remote to point to
Github.
git remote add origin https://github.com/userName/repoName.gitNow, when we go through the add, commit, push process of
staging and making a commit (as described above), you will be prompted
for your Github username and password.
you may also need to set some global options of your name and email address when first pushing to Github, but you will be instructed on how exactly to do this
Github allows for collaborative coding, meaning that people distributed across the world can work on different aspects of incredibly complicated things, including entire languages (e.g., Rust, Julia, etc.), machine learning frameworks (e.g., Tensorflow), and a large collection of operating systems (e.g., https://github.com/jubalh/awesome-os).
What does this mean for you?
Probably nothing, but it means something for how you will collaborate with your classmates, and how you will turn in assignments. All your dev work for your assignments will be version controlled on Github.
this will be done in class
sessionInfo()## R version 4.3.0 (2023-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] rmarkdown_2.22 sf_1.0-13 raster_3.6-20 sp_2.0-0 rgbif_3.7.7
##
## loaded via a namespace (and not attached):
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