#18: Development environments & workflows II

Maxime U Garcia ▸ @gau | @maxulysse
Karolinska Institutet | Science for Life Laboratory
Sweden

Overview

• 👷‍♀️ Working Best Practices
• Git + GitHub configuration
• 💻 VSCode configuration
• 💥 Local testing

Disclaimer

• My own work flow
  • Probably not the best

Working Best Practices

• ⏱️ ~20 min each morning on emails/Slack
• 🚶 Stand up at least 5 min every hour or so
• 🥤 Drink water
• 🔕 Avoid distractions
• ☕ Get some time for Fika

Git + GitHub configuration

• Set up your fork on GitHub
• 💾 Configure your local clone
• 🚀 Work on other people's code
• ♻️ Pull in updates

Git + GitHub configuration

Local clone setup

gh repo clone <username>/<repo>
cd <repo>

Git + GitHub configuration

Do work

git checkout -b <branch>_<new_feature>
git add <file>
git commit -m "feat: Did a thing"
git commit -m "fix: Fixed a thing"
git commit -m "chores: Had to do a thing"
git push -u origin <branch>_<new_feature>
gh pr create --base <branch> --title "<new_feature>" \
  --body "This <new_feature> is amazing and here's why..."

Git + GitHub configuration

Do tiny modifications

• On GitHub

Git + GitHub configuration

Keep code up to date locally

# Check for uncommitted changes
git status
# Pulls remote origin
git pull
# Fetch upstream and merge upstream branch on local
git fetch upstream; git merge upstream/<branch>

Git + GitHub configuration

Keep code up to date on GitHub

• On GitHub

VSCode configuration

• 👷‍♀️ Best Practices
• ⚒️ Useful plugins

VSCode configuration

• One main workspace
• One workspace for each repo

VSCode configuration

Plugins

• VSCode plugins: "nf-core-extensionpack" 🚀

Local testing

• 📃 Running tests locally
• 🐍 Pytest workflow locally

Spotify

Acknowledgements

Need help?

• bytesize 4:
  • GitHub contribution basics
• bytesize 11:
  • Development environments & workflows
• bytesize 17:
  • Pytest workflow

Get involved:
https://nf-co.re/join