command-line-cheatsheet

This document contains commonly used commands for

• GitHub
• Conda`
• conda-forge
• pip
• pre-commit
• Test PyPI
• Bash scripting

GitHub keyboard shortcuts

• G + I - visit issues
• G + P - visit PR
• G + A - visit Actions
• G + C - visit Code
• G + N - visit notification

GH notifications

• E Mark as done
• Shift + U - Mark as unread
• Shift + I - Mark as read
• Shift + M - Unsubscribe

GH Writing

• CMD + shift + P -toggle preview

GH Issue

• L - apply label
• Option + Shift + c - create a sub-issue
• C - create an issue from the list

GH keyboard help

• Shift + /

https://docs.github.com/en/get-started/accessibility/keyboard-shortcuts

Feel free to fork and add more useful commands and flags as needed.

Jupyer

• ESC + A/B/DD - Insert cell above/below/delete
• ESC + C/X/V - Copy/cut/paste
• ESC + O/shift+O - Hide/clear output
• Ctrl + Shift + (-) - split cell
• ESC + shift + M - merge selected cells
• ESC + L - show line number
• ESC + 0 + 0 - restart kernal

Vim

Cursor nav

• H - move to top of screen
• M - move to middle of screen
• L - move to bottom of screen
• 0 / $ - move cursor to beginning / end
• b / B - move word left, b but skip special chracters

Delete

• ctrl-W - delete word left

Edit

• D - delete everything on the right

• S - delete line and substitute text (same as cc)

• r - replace a single character.

• i - insert before the cursor

• I - insert at the beginning of the line

• A - insert (append) at the end of the line

• o - append (open) a new line below the current line

• O - append (open) a new line above the current line

• $d - From the current line to the end of the file

• 1d - From the current line to the beginning of the file

• dd - delete (cut) a line

• yy - yank (copy) a line

• u - undo

• U - restore (undo) last changed line

• . - repeat last command

• 5gg or 5G - go to line 5

• gg - go to the first line of the document

• zz - center cursor on screen

• zt - position cursor on top of the screen

• zb - position cursor on bottom of the screen

From: https://vim.rtorr.com/

Tool

Get the tree structure

brew install tree and run tree

GitHub

Git revert - for shared repositories undo or go back to the previous commit pushed to public and shared remote

Assume you have 2 commits, and the last commit is a mistake. The last commit is called "bad mistake". Use git revert HEAD to undo the last commit, but this generates a third commit called Revert "bad mistake". You can provide a specific commit ID for revert. An example from StackOverflow: assume you have four commit IDs 1, 2, 3, 4. If you run git revert 2, it returns the state at 3. This is the safe way since the commit history is preserved

Git reset - undo changes that have not been shared

“You should never use git reset when any snapshots after have been pushed to a public repository. After publishing a commit, you have to assume that other developers are reliant upon it.” - https://www.atlassian.com/git/tutorials/undoing-changes/git-reset

• Reset does not make commits.
• It changes the pointer to a commit

git reset resets Staging to the last commit. Use --hard to also reset files in your Working directory to the last commit.

HEAD~ is short for HEAD~1

soft does not change index (staging area) nor the files - but only the head

mixed/deafult changes the index but not the files

hard reset - resets index and working directory

# Delete remote branch
git push origin --delete cookierelease

# Delete local branch
git branch -D cookierelease

# Delete all branh
git branch | grep -v "main" | xargs git branch -D

# Delete all local tags
git tag -d $(git tag -l)

# Delete all remote tags
# git push origin --delete $(git tag -l)

Rest GitHub commit history (Know what you are done)

git checkout --orphan new-main HEAD~10
git add -A
git commit -m "Cleaned history: kept last 10 commits"
git branch -D main
git branch -m main
git push -f origin main

Git stash

# List all the stashes
$ git stash list
stash@{0}: WIP on admin_ui: 0c1a80a Removed annotation from JdbcAdminService, it is now explicity initialized in the applicationContext.
stash@{1}: WIP on admin_ui: 14e12e6 Added foreign keys for UserRole
stash@{2}: WIP on master: d188ecd Merge branch 'master' of semc-git:customercare
stash@{3}: WIP on master: 3763795 More work on user_details.
...

# Apply the latest stash, and remove it from the stack
$ git stash pop

# Apply a named patch, but leave it on the stack
$ git stash apply stash@{2} 

# Drop a stash
$ git stash drop stash@{3} 

# Clear the entire stash stack (almost never needed)
$ git stash clear

# A better way to purge the stash
$ git reflog expire --expire=30.days refs/stash

the `/refs/stash` file.

`git stash` does not commit but takes a snapshot of the local changes.

`git reset` creates a new commit point. It can jump back to any prior commit and also undo previous local changes.

`git stash save message` to add a custom message

`git stash push` also stash untracked files

`git stash pop` takes the files in the stash place and delete it from the histroy

`git stash show` inspect a summary

`git stash show diff` diff b/w a stashed change and the current state

`git stash apply` same as `git stash pop` but does not delete the history

`git stash list` displays history

`git stash drop` removes the latest stash

`git stash clear` removes all stashes

GitHub

You want to force sync with your forked remote branch

git fetch origin
git reset --hard origin/main

GitHub CLI

Show readme

# Show readme
gh repo view

# Open URL
gh browse

Pull request

# List
gh pr list
gh pr list --state open
gh pr list --state closed

# Status
gh pr checks 132

# Diff
gh pr diff 132

# Checkout
gh pr checkout 132

# Create
gh pr create
gh pr create --web
gh pr create --title "Fix codecov badge" --body "Closes #<issue number>"

# Review
gh pr review 132 --approve

Issue

# List
gh issue list
gh issue list --label bug

# Delete
gh issue delete 132
gh issue delete 132 --yes

# Create
gh issue create --web
gh issue create --title "Fix codecov badet unknown problem" --label "documentation" --body "Double check the secret value"

Workfow

# List available workflow(s)
gh workflow list

# View individual workflow
gh workflow view
gh workflow view check-news-item.yml --yaml

Git

Not covering basic ones suhc as checkout, pull, etc.

# Fetch all tags, branches, etc. without merging to your local branches
git fetch --all

# Add tag locally
git tag -a 0.1.3 -m "Test PyPI pre-release"

# Push tag to remote origin
git push origin 0.1.3

pip

# Install a list of packages in a file(s)
pip install -r requirements.txt
pip install -r pip.txt -r test.txt

# Install a specific version of a package
pip install bob==3.2

# Build and install your package to your environment
pip install .

# Build and install locally without using cache
pip install . --no-cache-dir

# Build and install locally without installing dependencies from metadata
pip install . --no-cache-dir --no-deps

# Build and install in development mode
# compiled binaries/extensions are located in the project folder, not the environment
pip install -e .

# Install a package from a .whl file
pip install bob-1.0.0-py3-none-any.whl

# Install a package from a source distribution (sdist) file
pip install https://example.com/package.tar.gz

Conda

Create an environment with Python 3.12:

conda create -n bob_env python=3.12
conda activate bob_env

Create an environment with specific Python, dependencies:

conda create -n diffpy_utils_env python=3.13 \
    --file requirements/test.txt \
    --file requirements/conda.txt \
    --file requirements/build.txt

For Apple Silicon (M1/M2, arm64), set the environmet as if running on an Intel-based macOS (osx-64):

CONDA_SUBDIR=osx-64 conda create -n diffpy_utils_env python=3.13 \
    --file requirements/test.txt \
    --file requirements/conda.txt \
    --file requirements/build.txt

Confirm your environment:

conda config --show subdir  #  osx-arm64

Install the latest pre-release package in the rc channel:

conda install -c conda-forge/label/bob_rc -c conda-forge bob

Install specific version of the conda package:

conda install bob-1.4.4rc3-py312h9fbc349_2

Add/remove a new channel:

# Add channel
conda config --add channels conda-forge/label/bob_rc

# Remove channel
conda config --remove channels conda-forge/label/bob_rc

Once install, do a quick import test:

python -c "import bob; print(bob.__version__)"

info

# List all available environments
conda env list

# Get info on current environment
conda info

# List packages installed
conda list
conda list -n bob

conda-forge

Only relevent for conda-forge users:

# Install
conda install -n root -c conda-forge conda-smithy

# Rerender
conda smithy rerender

# Lint the meta.yaml file
conda smithy recipe-lint

command-line shortcuts

Open up the shell configuration file using Visual Studio:

code  ~/.zshrc  # or ~/.bashrc

Activate the alias:

source ~/.zshrc  # or source ~/.bashrc

Sphinx preview

Use https://github.com/prkumar/sphinx-reload

pip install sphinx-reload
sphinx-reload docs

Test PyPI

# Build pakcage and upload to Test PyPI
python -m build && twine upload --repository testpypi dist/*

pre-commit

Run pre-commit

pre-commit run --all-files

Bash scripting

Bascis

The shebang line tells the system which interpreter to use to execute the script:

#!/bin/bash

Variable:

name="Bob"
echo "Hello world, $Bob!"

User inpput:

echo "What is your name?"
read name
echo "Hello, $name!"

For loop:

for i in {1..5}; do
    echo "Number $i"
done

Conditional statement:

echo "Enter a number:"
read num
if [ $num -lt 10 ]; then
    echo "The number is less than 10."
else
    echo "The number is 10 or greater."
fi

• gt for "greater than"
• eq for "equals"
• ne for "not equal"
• le for "less than or equal to"
• ge for "greater than or equal to"

While loop:

counter=1
while [ $counter -le 5 ]; do
    echo "Counter is $counter"
    ((counter++))
done

Function:

intro() {
    echo "Hi $1! You are $2 years old."
}
intro "Bob" 3

Folder/file management

# $# is a special variable giving the # of arguments
if [ "$#" -ne 1 ]; then
    exit 1
fi

# Use the first argument as the root directory
root_dir="$1/*"

# Loop through each item in the root directory
for dir in $root_dir; do
    if [ -d "$dir" ]; then  # Check if it's a directory
        echo "Visiting directory: $dir"
        # Perform operations in "$dir"
    fi
done

To use, run ./script.sh /path/to/directory.

Check a file exists:

# Check if a file exists
if [ ! -f "my_file.txt" ]; then
    echo "Error: File does not exist."
    exit 1
fi

exit 1 (or any non-zero value) indicates that the script is terminated with an error.

skpkg - Deploy sphinx doc via dispatch

name: Deploy Documentation

on:
  workflow_dispatch:

jobs:
  build-deploy:
      defaults:
        run:
          shell: bash -l {0}

      runs-on: ubuntu-latest
      steps:
        - name: Check out project
          uses: actions/checkout@v4
          with:
            ref: ${{ github.ref }}

        - name: Initialize miniconda
          uses: conda-incubator/setup-miniconda@v3
          with:
            activate-environment: build
            auto-update-conda: true
            environment-file: environment.yml
            auto-activate-base: false
            python-version: 3.13

        - name: Conda config
          run: >-
            conda config --set always_yes yes
            --set changeps1 no

        - name: Install  and docs requirements
          run: |
            conda install --file requirements/conda.txt
            conda install --file requirements/docs.txt
            python -m pip install -e . --no-deps

        - name: build documents
          run: make -C doc html

        - name: Deploy
          uses: peaceiris/actions-gh-pages@v4
          with:
            github_token: ${{ secrets.GITHUB_TOKEN }}
            publish_dir: ./doc/build/html

To see the rendered page,

https://htmlpreview.github.io/?https://github.com/bobleesj/scikit-package/gh-pages/index.html

References

• GitHub CLI https://cli.github.com/manual/