Ubuntu + Python + Git Terminal Cheat Sheet (DAMSL Edition)

📺 Table of Contents

• 📁 File & Directory Management
• 📄 File Viewing & Editing
• 🔍 Search & Navigation
• 🧰 System Utilities
• 📦 Package Management (APT)
• 🐍 Python & pyenv
• 🔐 SSH & Remote Access
  • Set up paswordless SSH} between 2 computers
  • Set up SSH for GitHub
  • Set up multiple keys
• 📡 FTP & File Transfer
• 🧠 Shortcuts
• 🌿 Git Essentials
  • Set up GitHub repos
• 🧹 Pre-commits
• 📝 NumPy Docstrings
• 📄 Generating Documentation
• 📽️ Reveal presentations

📁 File & Directory Management

Command	Description
ls	List files in current directory
ls -la	List all files with details
cd folder_name	Change directory
cd	Go to home directory
cd ..	Go up one directory
cd -	Go to previous directory
mkdir folder_name	Create a new folder
rm file	Delete file
rm -rf folder	Force delete folder and contents
cp source dest/	Copy file/folder
mv old new	Move or rename file/folder
touch file.txt	Create empty file

📄 File Viewing & Editing

Command	Description
cat file.txt	Show file contents
less file.txt	Scrollable view of file
nano file.txt	Edit file in nano editor
code .	Open folder in VS Code (if installed)

🔍 Search & Navigation

Command	Description
find . -name '*.py'	Find all .py files
grep "pattern" file.txt	Search for text in a file
grep -r "text" folder/	Recursive search in folder
pwd	Show current directory
history	View command history

🧰 System Utilities

Command	Description
whoami	Show current user
df -h	Show disk usage
free -h	Show memory usage
top / htop	Process monitor (install htop)
uptime	System uptime

📦 Package Management (APT)

Command	Description
sudo apt update	Refresh package index
sudo apt upgrade	Upgrade installed packages
sudo apt install pkgname	Install package
sudo apt remove pkgname	Remove package

🐍 Python & pyenv

Command	Description
python3 --version	Show system Python version
pyenv install 3.11.13	Install specific Python version
pyenv global 3.11.13	Set global Python version
pyenv local 3.11.13	Set version only for current folder
pyenv versions	List installed versions
pyenv which python	Show path to Python binary
poetry init	Create new Poetry project
poetry env use $(pyenv which python)	Link Poetry to pyenv Python
poetry env list	Lists all exiting environments
poetry env remove	Removes poetry environment
poetry add	Add dependency
poetry install	Install all libraries in toml
poetry shell	Activate project virtual environment

🔐 SSH & Remote Access

Command	Description
ssh user@host	Connect to remote machine
ssh -i ~/.ssh/id_rsa user@host	Use specific SSH key
ssh-keygen -t ed25519	Generate new SSH key
cat ~/.ssh/id_ed25519.pub	Show public key to add to GitHub/remote
scp file user@host:/remote/path	Copy file to remote server
scp user@host:/remote/file ./local/	Copy file from remote server

Set up passwordless SSH between 2 PCs

1. On local PC, generate new SSH key

ssh-keygen -t ed25519 -C "your_email@example.com"

Press enter to accept defaults.

If you are on Windows, your key is in C:/Users/User/.ssh

3. Copy key to remote computer

ssh-copy-id username@host_name

It’ll prompt for PC2 password once. After that, you're in passwordlessly.

4. SSH like usually

ssh username@host_name

It shouldn't ask you for a password.

Set up SSH for GitHub

1. On local PC, generate new SSH key

ssh-keygen -t ed25519 -C "your_email@example.com"

Press enter to accept defaults.

If you are on Windows, your key is in C:/Users/User/.ssh

2. Open the public key (.pub) and copy its contents
3. Got to GitHub $\rightarrow$ Settings $\rightarrow$ SSH and GPG keys $\rightarrow$ Add new key
4. Type a title (something to mark the specific computer) and paste in the key you copied

All set, now git remote should allow you to connect to your GitHub repos.

Set up different key for each connection

You can use the same SSH key for all your remote connections, but it is reccommended to set up different keys for each connection for security.

1. Generate keys for each purpose, ie.

ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519_github -C "your_email@example.com"
ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519_remote1 -C "remote1"
ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519_remote2 -C "remote2"

2. Add GitHub public key to GitHub (instructions)

3. Add each remote key's .pub to the respective PC using ssh-copy-id

ssh-copy-id -i ~/.ssh/id_ed25519_remote1.pub username@remote1_ip
ssh-copy-id -i ~/.ssh/id_ed25519_remote2.pub username@remote2_ip

4. Create (or edit) your .ssh-config file as follows:

# GitHub
Host github.com
  HostName github.com
  User git
  IdentityFile ~/.ssh/id_ed25519_github
  IdentitiesOnly yes

# Remote 1
Host remote1
  HostName remote1_ip
  User username
  IdentityFile ~/.ssh/id_ed25519_remote1
  IdentitiesOnly yes

# Remote 2
Host remote2
  HostName remote2_ip
  User username
  IdentityFile ~/.ssh/id_ed25519_remote2
  IdentitiesOnly yes

Now you can SSH all you want.

📡 FTP & File Transfer

Command	Description
ftp host	Connect to an FTP server
sftp user@host	Connect securely via SFTP
scp file user@host:/path	Copy file to remote server
scp user@host:/file ./	Copy file from remote server
rsync -avz file user@host:/path	Sync file/directory over SSH
rsync -avz user@host:/path ./	Download file/directory via rsync
mput *.txt	Upload multiple files in FTP
mget *.txt	Download multiple files in FTP
put file.txt	Upload file in FTP
get file.txt	Download file in FTP
bye	Exit FTP session

🧠 Shortcuts

Command	Description
Ctrl + C	Cancel current command
Ctrl + D	Exit terminal or virtual env
Ctrl + L	Clear terminal screen
↑ / ↓	Navigate command history
Tab	Autocomplete files or commands (use this like you life depends on it!)
!!	Repeat last command
Ctrl+	Move by word instead of character

🌿 Git Essentials

Command	Description
git init	Initialize a new Git repository
git config --global user.name/email	Set global Git username/email
git clone	Clone a remote repository
git status	Check status of working directory
git add	Stage changes for commit
git add .	Stage all changes
git diff	Shows unstaged changes
git diff --staged	Shows staged changes
git diff HEAD	Shows changes since last commit
git diff commit1 commit2	Shows changes between commits
git diff branch1 branch2	Shows changes between branches
git commit -m 'msg'	Commit staged changes with message
git commit --amend	Edit and replace the most recent commit.
git log	View commit history
git branch	List branches
git checkout	Switch to branch
git checkout -b	Create and switch to new branch
git merge	Merge branch into current
git pull	Fetch and merge from remote
git push	Push local commits to remote
git remote -v	List remote connections
git restore	Restore a file to its last commited state
git reset --soft HEAD~1	Undo the last commit, keep changes staged
git stash	Temporarily save uncommited changes
git stash pop	Apply and remove the most recent stash

Set up GitHub repos

There are 2 ways to set up a GitHub repo

1. Create a repo on GitHub and clone it locally
2. Create a repo locally and push it on GitHub

Create a repo on GitHub and clone it locally

1. Go to GitHub and create a repo. Name it and create a README.md. Oprionally select a template for the .gitignore, licence and description.
2. Once the the repo is created, go to Code $\rightarrow$ SSH and copy the repo SSH link.
3. On your local PC go to the folder you want to clone the repo in and open cmd/bash. 4.git clone link-you-copied

Your repo is cloned and ready for commits.

Create a repo locally and push to GitHub

Let's assume you have already created a repo, even made some commits already and want to upload to GitHub.

1. Go to GitHub and create a repo. Name it the same as your local repo and do not create a README.md (you already have one locally). You want your repo to be completely empty.
2. Once the the repo is created, go to Code $\rightarrow$ SSH and copy the repo SSH link.
3. Locally, on your cmd/bash do:

git remote add origin link-you-copied
git branch -M main
git push -u origin main

Your commits should be pushed to GitHub and your local repo is connected to the GitHub repo.

With GitHub CLI

1. Install GitHub CLI.
2. Connect it to you GitHub with gh auth login and follow the promts.
3. Create you local repo with git as usual and do the 1st commit.
4. gh repo create REPO_NAME --public --source=. --push to create a new GitHub repo and push your local repo.

🧹 Pre-commits

Pre-commits are scripts that run automatically before a commit is made. These can be used to ensure code quality by running linters, formatters, and other checks on the codebase.

🔧 Install & Set Up

poetry add pre-commit
pre-commit install

This adds the .pre-commit-config.yaml file, where you define the hooks you want to run.

📄 Example Configuration

Here's an example of a .pre-commit-config.yaml file:

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v3.4.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml
  - repo: https://github.com/psf/black
    rev: 21.12b0
    hooks:
      - id: black

🔄 Usage

• Stage files you want to commit.
• Run all hooks against all files: pre-commit run --all-files
• Run hooks only on changed files: pre-commit run
• Update pre-commit hooks: pre-commit autoupdate
• If you run git commit with pre-commits and files are modified by hooks, commit will be aborted. You need to:
  • Stage them again
  • Commit them

🪝 Linters

Analyze the code for syntax, style and potential bugs. Catch issues like:

• Unused variables
• Wrong import order
• Missing docstrings

🪝 Formatters

Automatically reformat code to follow a consistent style.

• Indentation
• Quote style
• Line breaks
• Comma placements

Linters and formatters get their config from pyproject.toml

📄 Example Configuration

[tool.ruff]
exclude = ["docs"]
line-length = 88
target-version = "py311"

[tool.ruff.lint]
ignore = [
  # pylint
  # No pylints
  # ruff
  "RUF001",
  # flake8-bandit
  "S101",
  ...
  "ISC001",
  "N806",
  "N803",
  "SLF001"
]
select = ["ALL"]

[tool.ruff.lint.flake8-quotes]
inline-quotes = "double"

[tool.ruff.lint.pydocstyle]
convention = "numpy"

📝 NumPy Docstrings

NumPy docstrings follow a specific format to ensure consistency and clarity. Here's a basic template for writing NumPy-style docstrings:

def example_function(param1, param2):
    """
    Brief summary of the function.

    Extended description of the function, which can cover
    multiple lines and provide more detailed information.

    Parameters
    ----------
    param1 : int
        Description of the first parameter.
    param2 : str
        Description of the second parameter.

    Returns
    -------
    bool
        Description of the return value.

    Raises
    ------
    ValueError
        If `param1` is not a positive integer.

    See Also
    --------
    related_function : Description of related function.
    
    Notes
    -----
    Additional notes about the function, its usage, or implementation details.

    Examples
    --------
    >>> example_function(3, 'test')
    True
    """

    if param1 <= 0:
        raise ValueError("param1 must be a positive integer")
    # Example function logic
    return True

Key Sections

• Summary: A one-line summary that starts with a capital letter and ends with a period.
• Parameters: A list of parameters with types and descriptions.
• Returns: Description of the return value, including type information.
• Raises: Any exceptions that the function may raise and the conditions under which they occur.
• See Also: References to related functions or methods within the module.
• Notes: Additional information about the function, which may include implementation details.
• Examples: Usage examples with the expected output, helpful for understanding function behavior.

📄 Generating Documentation

Assuming you already have numpy docstrings in your code.

1. Add necessary packages

poetry add --group docs numpydoc sphinx sphinx-rtd-theme sphinx-math-dollar myst-parser

• numpydoc: Parses NumPy-style docstrings for Sphinx.
• sphinx: Turns reStructuredText or Markdown + docstrings into HTML, LaTeX, PDF, etc.
• sphinx-math-dollar: Allows you to write math equations with LaTeX dollar signs ($...$ for inline, $$...$$ for block).
• sphinx-rtd-theme: The ReadTheDocs theme
• myst-parser: Enables writing docs in Markdown .md instead of .rst

2. Set up sphinx in the docs folder of your repo

poetry run sphinx-quickstart docs

Follow prompts on the terminal.

3. Configure conf.py For example

# -- General configuration ---------------------------------------------------

extensions = [
    "sphinx.ext.autosummary",
    "sphinx.ext.autodoc",
    "numpydoc",
    "sphinx_math_dollar",
    "sphinx.ext.mathjax",
    "sphinx_rtd_theme",
    "myst_parser",  # enables Markdown support via MyST
]

templates_path = ["_templates"]
exclude_patterns = []

autosummary_generate = True
numpydoc_class_members_toctree = False

# -- Options for HTML output -------------------------------------------------

html_theme = "sphinx_rtd_theme"

# -- Options for napoleon extension ------------------------------------------
napoleon_google_docstring = False
napoleon_numpy_docstring = True

4. Autogenerate .rst files for your code

sphinx-apidoc -o docs/source your_module

5. Include modules into index.rst Include something like:

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   your_module # don't forget the indent

6. 📚 Build your documentation

sphinx-build -b html docs/source docs/build

📽️ Reveal presentations

Get template from githug aramp

Create local server with npm slides.md

Command	Description
---	Create new slide to the right
--	Create new slide downwards

To deploy changes online:

• Push to GitHub
• On the GitHub repo go to Settings $\rightarrow$ Pages
• Source: Deploy from a branch
• Branch: main
• Folder: /root
• Click Save