SKC CI Workshop June 2024

"Getting started with Cyberinfrastructure"

https://gitea.skc.edu/workshops

Lessons

Lessons (Day 1):

• Welcome and overview
• Introduction to Jupyter Notebooks, RStudio, and Git
• R for Reproducible Scientific Analysis
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/01-rstudio-intro.html
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/04-data-structures-part1.html
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/05-data-structures-part2.html
    • Data: https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/main/episodes/data/gapminder_data.csv
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/06-data-subsetting.html
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/08-plot-ggplot2.html
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/09-vectorization.html
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/11-writing-data.html
  • https://swcarpentry.github.io/r-novice-gapminder/instructor/15-wrap-up.html

Lessons (Day 2):

• Welcome and overview
• Sharing & collaborating with code (Github introduction)
  • https://swcarpentry.github.io/git-novice/01-basics.html
    • Motivation: https://happygitwithr.com/big-picture.html (extra background)
  • https://swcarpentry.github.io/git-novice/04-changes.html
  • https://swcarpentry.github.io/git-novice/05-history.html
  • https://swcarpentry.github.io/git-novice/06-ignore.html
  • https://swcarpentry.github.io/git-novice/08-collab.html
  • https://swcarpentry.github.io/git-novice/09-conflict.html (optional)
  • https://swcarpentry.github.io/git-novice/10-open.html
  • https://swcarpentry.github.io/git-novice/11-licensing.html
• Technical overview of the infrastructure.

Workshop Links:

• CI environment (SKC-CARE): https://ci.skc.edu/
• Git environment: https://gitea.skc.edu
• Workshop site: https://gitea.skc.edu/workshops/2024-June-CI-Workshop
• Workshop Gitea organization: https://gitea.skc.edu/2024-June-CI-Workshop
• Instructor Notes: Notes.md
• Class Notes: https://gitea.skc.edu/Workshops/2024-June-CI-Workshop-In-Class

Resources

• Git and R (recommended for students and as a teaching resource): https://happygitwithr.com/
  • Introduction: https://dx.doi.org/10.7287%2Fpeerj.preprints.3159v2
• R Markdown: https://bookdown.org/yihui/rmarkdown/markdown-syntax.html
• R Tutorial: https://www.cyclismo.org/tutorial/R/
• ggplot2: https://ggplot2.tidyverse.org/
• ggplot2 cheat-sheet: https://www.maths.usyd.edu.au/u/UG/SM/STAT3022/r/current/Misc/data-visualization-2.1.pdf
• Git book: https://git-scm.com/book/en
• Git branching:
  • https://happygitwithr.com/git-branches (and remotes https://happygitwithr.com/git-remotes)
  • https://nvie.com/posts/a-successful-git-branching-model/
  • https://git-scm.com/book/en/v2/Git-Branching-Branches-in-a-Nutshell
• R project introduction http://cran.r-project.org/doc/manuals/R-intro.html
• R Language: https://www.r-project.org/

Advanced Materials

• Git internals: "Git for Ages 4 And Up" - https://youtu.be/1ffBJ4sVUb4
• Test Driven Development (TDD) http://www.agiledata.org/essays/tdd.html