Appendix D — Cheat Sheets

Environments as code

Check library and repository status

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

Create and use a standalone project library

Make sure you’re in a standalone project library.

Step	R Command	Python Command
Create a standalone library.	`renv::init()` Tip: get `{renv}` w/ `install.packages("renv")`.	`python -m venv <dir>` Convention: use `.venv` for `<dir>`
Activate project library.	`renv::activate()` Tip: happens automatically in RStudio project.	`source <dir> /bin/activate`
Install packages as normal.	`install.packages("<pkg>")`	`python -m pip install <pkg>`
Snapshot package state.	`renv::snapshot()`	`pip freeze > requirements.txt`
Exit project environment.	Leave R project or `renv::deactivate()`	`deactivate`

Collaborate on someone else’s project

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

Step	R Command	Python Command
Move into the project directory.	`setwd("<project-dir>")` Or open the project in RStudio.	`cd <project-dir>`
Create a project environment.	`renv::init()`	`python -m venv <dir>` Convention: use `.venv` for `<dir>`
Enter a project environment.	Happens automatically or `renv::activate()`.	`source <dir> /bin/activate`
Restore packages.	Happens automatically or `renv::restore()`.	`pip install -r requirements.txt`

HTTP codes

As you work with HTTP traffic, you’ll learn some of the common codes. Here’s are some of those used most frequently.

Code	Meaning
\(200\)	Everyone’s favorite, a successful response.
\(\text{3xx}\)	Your query was redirected somewhere else, usually ok.
\(\text{4xx}\)	Errors with the request.
\(400\)	Bad request. This isn’t a request the server can understand.
\(401\)/\(403\)	Unauthorized or forbidden. Required authentication hasn’t been provided.
\(404\)	Not found. There isn’t any content to access here.
\(\text{5xx}\)	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.

Git

All commands run prefixed with git

Command	What It Does
`clone <remote>`	Clone a remote repo (use the SSH URL).
`add <files/dir>`	Add files/directory to staging area.
`commit -m <message>`	Commit staging area.
`push origin <branch>`	Push to a remote.
`pull origin <branch>`	Pull from a remote.
`checkout <branch name>`	Check out a branch.
`checkout -b <branch name>`	Create and check out a branch.
`branch -d <branch name>`	Delete a branch.

Docker

Docker CLI commands

All prefixed with docker.

Stage	Command	What It Does	Notes and Helpful Options
Build	`build <directory>`	Builds a directory into an image.	`-t <name:tag>` provides a name to the container. `tag` is optional, defaults to `latest`.
Move	`push <image>`	Push a container to a registry.
Move	`pull <image>`	Pull a container from a registry.	Rarely needed because `run` pulls the container if needed.
Run	`run <image>`	Run a container.	See flags in next table.
Run	`stop <container>`	Stop a running container.	`docker kill` can be used if `stop` fails.
Run	`ps`	List running containers.	Useful to get container `id`.
Run	`exec <container> <command>`	Run a command inside a running container.	Basically always used to open a shell with `docker exec -it <container> /bin/bash`
Run	`logs <container>`	Views logs for a container.

Flags for `docker run`

Flag	Effect	Notes
`--name <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 <port>:<port>`	Publish port from inside running 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>.

Dockerfile commands

These commands 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 .`

Cloud services

Service	AWS	Azure	GCP
Kubernetes	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

Command line

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).

Linux filesystem navigation

Command	What It Does/Is	Notes and 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` to format as a list, `-a` for all (include hidden files that start with `.`)
`pwd`	Print working directory.
`cd <dir>`	Change working directory to `<dir>`	Can use relative or absolute paths.

Reading text files

Command	What It Does/Is	Notes and Helpful Options
`cat <file>`	Print a file from the top.
`less <file>`	Print a file, but just a little.	Useful to look at a few rows of `.csv` files. Can be much faster than `cat` for big files.
`head <file>`	Look at the beginning of a file.	Defaults to 10 lines, specify with `-n <n >`.
`tail <file>`	Look at the end of a file.	Useful for logs where the newest part is last. Use the `-f` flag to follow a live view.
`grep <expression>`	Search a file using reg ex.	Test regex on \(\text{regex101.com}\). Useful in combination with the pipe.
`\|`	The pipe.
`wc <file>`	Count the words in a file.	Use `-l` to count lines, useful for `.csv` files.

Manipulating files

Command	What It Does/Is	Notes and Helpful Options
`rm <path>`	Remove.	`-r` to recursively remove everything below a file path. `-f` for force to skip asking for each file. Be very careful, it’s permanent!
`cp <from> <to>`	Copy.
`mv <from> <to>`	Move.
`*`	Wildcard.
`mkdir`/`rmdir`	Make/remove directory.	`-p` to create any parts of path that don’t exist.

Move things to/from server

Command	What It Does	Notes and Helpful Options
`tar`	Create/extract archive file.	Almost always used with flags. Create is usually `tar -czf <archive> <file(s)>`. Extract is usually `tar -xfv <archive>`.
`scp`	Secure copy via `ssh`.	Run from laptop. You can use most `ssh` flags, like `-i` and `-v`.

Write files from the command line

Command	What It Does	Notes
`touch`	Creates file if it doesn’t 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.

Command line text editors (Vim and Nano)

Command	What It Does	Notes and Helpful Options
`^`	Prefix for file command in `nano` editor.	It’s the Apple `Command` or Windows `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.

SSH

General usage:

Terminal

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.

Linux admin

Users

Command	What It Does	Notes and Helpful Options
`su <username>`	Change to be a different user.
`whoami`	Get username of current user.
`id`	Get full user and group info on current user.
`passwd`	Change password.
`useradd`	Add a new user.
`usermod <username>`	Modify user `username`.	`-aG <group>` adds to a group (e.g., `sudo`)

Permissions

Command	What It Does	Notes and Helpful Options
`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`.
`chown <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.

Install applications (Ubuntu)

Command	What It Does
`apt-get update && 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.

Storage

Command	What It Does	Notes and 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 `du -h <dir> \| sort -h`. Also useful to combine with `head`.

Processes

Command	What It Does	Notes and 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.

Networking

Command	What It Does	Notes and Helpful Options
`netstat`	See ports and services using them.	Usually used with `-tlp`, to get `tcp` listeners with their `pid`s.
`ssh -L <port>:localhost:<port>:<host>`	Forwards a port on remote `<host>` to local.	Choose local port to match remote port.

The path

Command	What It Does
`which <command>`	Finds the location of the binary for `command`.
`ln -s <linked location> <where to put symlink>`	Creates a symlink.

`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.

IP Addresses and ports

Special IPv4 Addresses

Address	Meaning
\(127.0.0.1\)	`localhost` or loopback, the machine that originated the request.
\(\text{10.x.x.x}\), \(\text{172.16.x.x}\), \(\text{172.31.x.x}\), \(\text{192.168.x.x}\)	Protected address blocks used for private IP addresses.

Special ports

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

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