Appendix D — Cheatsheets

D.1 Environments as Code

D.1.1 Checking library + repository status

Step	R Command	Python Command
Check whether library in sync with lockfile.	`renv::status()`	None

D.1.2 Creating and Using a Standalone Project Library

Make sure you’re in a standalone project library.

Step	R Command	Python Command
Create a standalone library. Tip: Make sure you’ve got `{renv}`/`{venv}`: `in stall.packages("renv")` `{venv}` included w/ Python 3.5+	`renv::init()`	`python -m venv <dir>` Convention: use`.venv` for `<dir>`
Activate project library.	`renv::activate()` Happens automatically if in RStudio project.	`source <dir> /bin/activate`
Install packages as normal.	`install.p ackages("<pkg>")`	`python -m pip install <pkg>`
Snapshot package state.	`renv::snapshot()`	`pip freez e > requirements.txt`
Exit project environment.	Leave R project or `re nv::deactivate()`	`deactivate`

D.1.3 Collaborating on someone else’s project

Start by downloading the project into a directory on your machine.

Step	R Command	Python Command
Move into project directory.	`set wd ("< project-dir>")` Or open project in RStudio.	`cd <project-dir>`
Create project environment.	`renv::init()`	`python -m venv <dir>` Recommend: use `.venv` for `<dir>`
Enter project environment.	Happens automatically or `re nv::activate()`	`source <dir> /bin/activate`
Restore packages.	Happens automatically or `r env::restore()`	`pi p install -r requirements.txt`

D.2 HTTP Code Cheatsheet

As you work more with HTTP traffic, you’ll learn some of the common codes. Here’s a cheatsheet for some of the most frequent you’ll see.

Code	Meaning
`200`	Everyone’s favorite, a successful response.
`3xx`	Your query was redirected somewhere else, usually ok.
`4xx`	Errors with the request
`400`	Bad request. This isn’t a request the server can understand.
`401` and `403`	Unauthorized or forbidden. Required authentication hasn’t been provided.
`404`	Not found. There isn’t any content to access here.
`5xx`	Errors with the server once your request got there.
`500`	Generic server-side error. Your request was received, but there was an error processing it.
`504`	Gateway timeout. This means that a proxy or gateway between you and the server you’re trying to access timed out before it got a response from the server.

D.3 Git

Command	What it does
`git clone <remote>`	Clone a remote repo – make sure you’re using SSH URL.
`git add <files/dir>`	Add files/dir to staging area.
`git commit -m <message>`	Commit staging area.
`git p ush origin <branch>`	Push to a remote.
`git p ull origin <branch>`	Pull from a remote.
`git che ckout <branch name>`	Checkout a branch.
`git checko ut -b <branch name>`	Create and checkout a branch.
`git bran ch -d <branch name>`	Delete a branch.

D.4 Docker

D.4.1 Docker CLI Commands

S ta ge	Command	What it does	Notes and helpful options
B ui ld	`docker b uild <directory>`	Builds a directory into an image.	`-t <name:tag>` provides a name to the container. `tag` is optional, defaults to `latest`.
Mo ve	`doc ker push <image>`	Push a container to a registry.
Mo ve	`doc ker pull <image>`	Pull a container from a registry.	Rarely needed because `run` pulls the container if needed.
R un	`do cker run <image>`	Run a container.	See flags in next table.
R un	`docker stop <container>`	Stop a running container.	`docker kill` can be used if `stop` fails.
R un	`docker ps`	List running containers.	Useful to get container `id` to do things to it.
R un	`docker exec <cont ainer> <command>`	Run a command inside a running container.	Basically always used to open a shell with `docker exec -it <container> /bin/bash`
R un	`docker logs <container>`	Views logs for a container.

D.4.2 Flags for `docker run`

Flag	Effect	Notes
`--n ame <name>`	Give a name to container.	Optional. Auto-assigned if not provided
`--rm`	Remove container when its stopped.	Don’t use in production. You probably want to inspect failed containers.
`-d`	Detach container (don’t block the terminal).	Almost always used in production.
`-p <po rt>:<port>`	Publish port from inside running inside container to outside.	Needed if you want to access an app or API inside the container.
`-v< dir>:<dir>`	Mount volume into the container.

Reminder: Order for -p and -v is <host>:<container>

D.4.3 Dockerfile Commands

These are the commands that go in a Dockerfile when you’re building it.

Command	Purpose	Example
`FROM`	Indicate base container.	`FROM rocker/r-ver:4.1.0`
`RUN`	Run a command when building.	`RUN apt-get update`
`COPY`	Copy from build directory into the container.	`COPY . /app/`
`CMD`	Specify the command to run when the container starts.	`CMD quarto render .`

D.5 Cloud Services

Service	AWS	Azure	GCP
Kubernetes cluster	EKS or Fargate	AKS	GKE
Run a container or application	ECS or Elastic Beanstalk	Azure Container Apps	Google App Engine
Run an API	Lambda	Azure Functions	Google Cloud Functions
Database	RDS	Azure SQL	Google Cloud Database
Data Warehouse	Redshift	DataLake	BigQuery
ML Platform	SageMaker	Azure ML	Vertex AI
NAS	EFS or FSx	Azure File	Filestore

D.6 Command Line

D.6.1 General Command Line

Symbol	What it is
`man <command>`	Open manual for `command`
`q`	Quit the current screen
`\`	Continue bash command on new line
`ctrl + c`	Quit current execution
`echo <string>`	Print string (useful for piping)

D.6.2 Linux Navigation

Command	What it does/is	Notes + Helpful options
`/`	System root or file path separator
`.`	current working directory
`..`	Parent of working directory
`~`	Home directory of the current user
`ls <dir>`	List objects in a directory	`-l` - format as list `-a` - all (include hidden files that start with `.`)
`pwd`	Print working directory
`cd <dir>`	Change directory	Can use relative or absolute paths

D.6.3 Reading Text Files

Command	What it does	Notes + Helpful options
`cat <file>`	Print a file from the top.
`less <file>`	Print a file, but just a little.	Can be very helpful to look at a few rows of csv. Lazily reads lines, so can be much faster than `cat` for big files.
`head <file>`	Look at the beginning of a file.	Defaults to 10 lines, can specify a different number with `-n <n>`.
`tail <file>`	Look at the end of a file.	Useful for logs where the newest part is last. The `-f` flag is useful to follow for a live view.
`gre p <expression>`	Search a file using regex.	Writing regex can be a pain. I suggest testing on \(\text{regex101.com}\). Often useful in combination with the pipe.
`\|`	The pipe
`wc <file>`	Count words in a file	Use `-l` to count lines, useful for `.csv` files.

D.6.4 Manipulating Files

Command	What it does	Notes + Helpful Options
`rm <path>`	Remove	`-r` - recursively remove everything below a file path `-f` - force - don’t ask for each file Be very careful, it’s permanent

`c p <from> <to>`	Copy
`m v <from> <to>`	Move
`*`	Wildcard
`mkdir`/`rmdir`	Make/remove directory	`-p` - create any parts of path that don’t exist

D.6.5 Move things to/from server

Command What it does Notes + Helpful Options

tar

Create/extract archive file

Almost always used with flags.

Create is usually tar -czf <a rchive name> <file(s)>

Extract is usually t ar -xfv <archive name>

scp

Secure copy via ssh

Run on laptop to server

Can use most ssh flags (like -i and -v)

D.6.6 Write files from the command line

Command	What it does	Notes
`touch`	Creates file if doesn’t already exist.	Updates last updated to current time if it does exist.
`>`	Overwrite file contents	Creates a new file if it doesn’t exist
`>>`	Concatenate to end of file	Creates a new file if it doesn’t exist

D.6.7 Command Line Text Editors (Vim + Nano)

Command	What it does	Notes + Helpful options
`^`	Prefix for file command in `nano` editor.	Its the `⌘` or `Ctrl` key, not the caret symbol.
`i`	Enter insert mode (able to type) in `vim`
`escape`	Enter normal mode (navigation) in `vim`.
`:w`	Write the current file in `vim` (from normal mode)	Can be combined to save and quit in one, `:wq`
`:q`	Quit `vim` (from normal mode)	`:q!` quit without saving

D.7 `ssh`

ssh <user>@<host>

Flag	What it does	Notes
`-v`	Verbose, good for debugging.	Add more `v`s as you please, `-vv` or `-vvv`.
`-i`	Choose identity file (private key)	Not necessary with default key names.

D.8 Linux Admin

D.8.1 Users

Command	What it does	Helpful options + notes
`s u <username>`	Change to be a different user.
`whoami`	Get username of current user.
`id`	Get full user + group info on current user.
`passwd`	Change password.
`useradd`	Add a new user.
`usermo d <username>`	Modify user `username`	`-aG <group>` adds to a group (e.g. `sudo`)

D.8.2 Permissions

Command	What it does	Helpful options + notes
`chmod <permissions> <file>`	Modifies permissions on a file or directory.	Number indicates permissions for user, group, others: add `4` for read, `2` for write, `1` for execute, `0` for nothing, e.g. `644`.
`chow n <user/group> <file>`	Change the owner of a file or directory.	Can be used for user or group, e.g. `:my-group`.
`sudo <command>`	Adopt root permissions for the following command.

D.8.3 Install applications (Ubuntu)

Command	What it does
`apt-get u pdate && apt-get upgrade -y`	Fetch and install upgrades to system packages
`apt-get install <package>`	Install a system package.
`wget`	Download a file from a URL.
`gdebi`	Install local `.deb` file.

D.8.4 Storage

Command What it does Helpful options

df Check storage space on device. -h for human readable file sizes.

Command	What it does	Helpful options
`df`	Check storage space on device.	`-h` for human readable file sizes.
`du`	Check size of files.	Most likely to be used as `d u - h <dir> \| sort -h` Also useful to combine with `head`.

du

Check size of files.

Most likely to be used as d u - h <dir> | sort -h

Also useful to combine with head.

D.8.5 Processes

Command	What it does	Helpful options
`top`	See what’s running on the system.
`ps aux`	See all system processes.	Consider using `--sort` and pipe into `head` or `grep`
`kill`	Kill a system process.	`-9` to force kill immediately

D.8.6 Networking

Command What it does Helpful Options

netstat See ports and services using them. Usually used with -tlp, for tcp listening applications, including pid

ssh -L <port>:<i p>:<port>:<host>

Port forwards a remote port on remote host to local.

Remote ip is usually localhost.

Choose local port to match remote port.

D.8.7 The path

Command	What it does
`which <command>`	Finds the location of the binary that runs when you run `command`.
`ln -s <location to l ink>:<location of symlink>`	Creates a symlink from file at `location to link` to `location of symlink`.

D.8.8 `systemd`

Daemonizing services is accomplished by configuring them in /etc/systemd/system/<service name>.service.

The format of all commands is systemctl <command> <application>.

Command	Notes/Tips
`status`	Report status
`start`
`stop`
`restart`	`stop` then `start`
`reload`	Reload configuration that doesn’t require restart (depends on service)
`enable`	Daemonize the service
`disable`	Un-daemonize the service

D.9 IP Addresses and Ports

D.9.1 Special IP Addresses

Address	Meaning
\(\text{127.0.0.1}\)	\(\text{localhost}\) or loopback – the machine that originated the request.
\(\text{192.168.x.x}\) \(\text{172.16.x.x.x}\) \(\text{10.x.x.x}\)	Protected address blocks used for private IP addresses.

\(\text{127.0.0.1}\)

\(\text{localhost}\) or loopback – the machine that originated the request.

\(\text{192.168.x.x}\)

\(\text{172.16.x.x.x}\)

\(\text{10.x.x.x}\)

Protected address blocks used for private IP addresses.

D.9.2 Special Ports

All ports below \(1024\) are reserved for server tasks and cannot be assigned to admin-controlled services.

Protocol/Application	Default Port
HTTP	\(80\)
HTTPS	\(443\)
SSH	\(22\)
PostgreSQL	\(5432\)
RStudio Server	\(8787\)
Shiny Server	\(3939\)
JupyterHub	\(8000\)