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<a href="https://www.nf-co.re"><img src="https://raw.githubusercontent.com/nf-core/logos/master/byte-size-logos/bytesize-darkbg.svg" width="60%"><img></a>
## \#18: Development environments & workflows II
Maxime U Garcia ▸ [<i class="fa fa-twitter" aria-hidden="true"></i>@gau](https://twitter.com/gau/) | [<i class="fa fa-github" aria-hidden="true"></i>@maxulysse](https://github.com/maxulysse/)
Karolinska Institutet | Science for Life Laboratory
Sweden
---
## Overview
- 👷♀️ Working Best Practices
- <i class="fa fa-github" aria-hidden="true"></i> 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
- <i class="fa fa-github" aria-hidden="true"></i> 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
```bash
gh repo clone <username>/<repo>
cd <repo>
```
---
## Git + GitHub configuration
Do work
```bash
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
```bash
# 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"**_](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) 🚀
---
## Local testing
- 📃 Running tests locally
- 🐍 Pytest workflow locally
---
## Spotify
[<i class="fa fa-spotify" aria-hidden="true"></i>](https://open.spotify.com/playlist/6LyhtB3bllSwNbK9iDNVgH?si=eaf6b95eac934e71)
---
## Acknowledgements
<img src="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/acknowledgments_2021_dark.svg" title="Institutes acknowledgements" alt="Institutes acknowledgements"/>
---
<a href="https://nf-co.re/community#organisations">
<img src="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/institutes_2021_dark.svg" title="Institutes acknowledgements" alt="Institutes acknowledgements"/>
</a>
---
<a href="https://nf-co.re/community#contributors">
<img src="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/slides/nf-core_contributors_2021_03.png" title="Contributors acknowledgements" alt="Contributors acknowledgements"/>
</a>
---
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## Need help?
- bytesize 4:
- [GitHub contribution basics](https://nf-co.re/events/2021/bytesize-4-github-contribution-basics)
- bytesize 11:
- [Development environments & workflows](https://nf-co.re/events/2021/bytesize-11-dev-envs-workflows)
- bytesize 17:
- [Pytest workflow](https://nf-co.re/events/2021/bytesize-17-pytest-workflow)
Get involved:
[https://nf-co.re/join](https://nf-co.re/join)
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