Happy Git and GitHub for the useR @JennyBryan @STAT545 @jennybc - - PowerPoint PPT Presentation

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Happy Git and GitHub for the useR @JennyBryan @STAT545 @jennybc - - PowerPoint PPT Presentation

Dec 16, 2023 1.11k likes •1.81k views

Happy Git and GitHub for the useR @JennyBryan @STAT545 @jennybc stat545-ubc.github.io happygitwithr.com Slides used in live workshops based on: happygitwithr.com Given the self-guided CSAMA lab format heres a little guidance for

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@JennyBryan @jennybc

Happy Git and GitHub for the useR

@STAT545 stat545-ubc.github.io

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happygitwithr.com

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Slides used in live workshops based on: happygitwithr.com

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Given the self-guided CSAMA lab format … here’s a little guidance for you. Optional: read Why Git? Why GitHub? Optional: look at the rest of these slides. Prove you exist and have a GitHub account 🙃

  • Put an emoji on this GitHub issue:

CSAMA lab participants: What is your operating system? Complete everything in these sections of happygitwithr.com

  • Installation
  • Connect Git, GitHub, RStudio
  • Get help from us if you need it! Setup is half the battle here.
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Given the self-guided CSAMA lab format … here’s a little guidance for you. Depending on your background and ambitions … Do something from Early Usage section:

  • New project, GitHub first
  • Existing project, GitHub first
  • Existing project, GitHub last

Or choose something more advanced from Tutorial prompts section:

  • Clone a repo
  • Fork a repo
  • Create a bingo card … maybe for CSAMA?
  • Practice failure: burn it all down
  • Search GitHub … maybe Bioconductor specific searches?
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Version control systems (VCS) were created to help groups of people develop software Git, in particular, is being “repurposed” for activities

  • ther than pure software development … like the

messy hybrid of writing, coding and data wrangling … and exposing the gory details… and collaborating with others

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What would Git adoption feel like?

Install Git. Configure it. Affirm RStudio can find it. R project? Pre-existing or new. Dedicate a directory to it. Make that an RStudio Project. Make that a Git repository. Do your usual thing but … instead of just saving, you also make commits. Push to GitHub periodically.

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RStudio will offer a Git pane to help you make commits, view history and diffs, and push to / pull from GitHub.

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You — and possibly other people! — could visit the project on GitHub. For browsing and much more.

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Do this now:

Put an emoji on this GitHub issue: CSAMA lab participants: What is your operating system?

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Our battle-tested installation instructions:

happygitwithr.com

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By now you should have done this: Complete everything in these sections of happygitwithr.com

  • Installation
  • Connect Git, GitHub, RStudio
  • Get help from us if you need it! Setup is half the battle here.
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https://github.com/Lokaltog/git-man-page-generator https://git-man-page-generator.lokaltog.net

highly recommended stress relief

http://www.commitlogsfromlastnight.com http://starlogs.net

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This is a good time to Explore some of the comic relief resources, so you can find them again when Git despair strikes.

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agony : flow

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agony : flow

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agony reduction

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Use a Git client

RStudio might not be enough — some noticeable gaps I 💘 SourceTree (free, Mac OS + Windows) More recommendations here: http://happygitwithr.com/git-client.html

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SourceTree, a free Git client for Windows and Mac.

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Or do it like this … it’s your call.

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RStudio can also act as your Git(Hub) client

http://www.rstudio.com/ide/docs/version_control/overview

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This is a good time to do: From Installation:

  • Install a Git client.

From Early Usage section:

  • New project, GitHub first
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Use GitHub

Or Bitbucket or Gitlab or … Even if you keep things private and don’t collaborate. Commit and push early and often! Why, you ask?

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  • Alberto Brandolini
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The amount of Git skilz necessary to fix a borked up repo is an order of magnitude bigger than to bork it.

  • Me
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burn it all down

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If that doesn't fix it, git.txt contains the phone number of a friend of mine who understands

  • git. Just wait through a

few minutes of 'It's really pretty simple, just think

  • f branches as...' and

eventually you'll learn the commands that will fix everything.

“burn it all down” workflow

  • n explainxkcd.com
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This is a good time to do: From Tutorial prompts section:

  • Practice failure: burn it all down
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increase flow

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machine readable & human readable

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code

can be machine & human readable

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data

can be machine & human readable

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your project

can be machine & human readable

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code comments README explanation-of- mystifying- variable-names- and-codes.txt

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What is here? When did it last change? Who changed it? Why did they change it? Can I have it? Oh, I want that other version.

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Commits are how the files evolve

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Commit message = short description of what/why changed

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“diffs” show what actually changed

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Issues for bug reports, feature requests, to do list, …

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This is a good time to Find a package you use that is developed on GitHub Explore its code, releases, and issues

  • r

Find a data analytical project you find interesting on GitHub Explore its code! Maybe run it! FiveThirtyEight shares data and code behind its stories and interactives at on GitHub https://github.com/fivethirtyeight/data

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collaboration

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in theory more typical GitHub

adapted from https://www.atlassian.com/git/tutorial/git-basics#!clone

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Note the contributions to STAT 545 materials from one prof, 3 TAs, and one kind soul from the internet

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“Pull requests” are a mechanism to propose, discuss, and merge changes into a repository.

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when you’re the boss: link to evolving files, don’t attach static copies to email plain text everything you can use Git put it on the internet somewhere when you’re not the boss: try to talk everyone into Google Docs 😊

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get a pseudo- website for free

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The unreasonable effectiveness of GitHub browsability

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Impressive showing by Git here

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Comma (.csv) and tab (.tsv) delimited files are automatically rendered nicely in GitHub repositories Example: some Lord of the Rings data

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When rendered Markdown is no longer enough …

<my_thing>.github.io

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When we push *.html to STAT 545 repo, website updates!

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the poor woman’s regression test of a data analysis

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Your code’s the same Your data’s the same But you updated R + pkgs Surprise!

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subtle fig changes due to ggplot2 release