command-line-cheatsheet

This document contains commonly used commands for

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

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

GitHub

# Delete remote branch
git push origin --delete cookierelease

# Delete local branch
git branch -D cookierelease

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

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

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

Copy the following to the file:

# My custom aliases, appliy via source ~/.zshrc
alias ga='git add'
alias gc='git checkout'
alias gpum='git pull upstream main'
alias grau='git remote add upstream'
alias gfa='git fetch --all'
alias grv='git remote -v'
alias gcm='git commit -m'
alias gcb='git checkout -b'
alias gp='git pull'
alias gpo='git push origin'
alias gl='git log'
alias gs='git status'
alias gd='git diff'
alias gb='git branch'
alias gr='git restore'

# github CLI
alias ghpr='gh pr create'
alias ghprl='gh pr list'
alias ghprc='gh pr checkout'
alias ghil='gh issue list'
alias ghb='gh browse'

# install
alias pi='pip install'
alias ci='conda install'

# test
alias pt='pytest'

# format
alias pc='pre-commit run --all-files'

# build
alias pb='python -m build'

# dist
alias testpypi='twine upload --repository testpypi dist/*'

Activate the alias:

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

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.

References

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