DFCI Introduction to Git and GitHub

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Introduction to Git and GitHub Patrick Kimes, PhD Postdoctoral Fellow Dana-Farber Cancer Institute Harvard TH Chan School of Public Health Data Science Seminar November 27, 2018

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why care about Git and GitHub?

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why care about Git and GitHub? sharing collaboration version control

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Git software for managing ﬁles in a folder (repo)

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GitHub Git software for managing ﬁles in a folder (repo) GitHub cloud service for hosting Git repos

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GitHub GitHub cloud service for hosting Git repos /somewhere/on/my/computer/sigclust2/ https://github.com/pkimes/sigclust2/ Git software for managing ﬁles in a folder (repo)

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GitHub Git software for managing ﬁles in a folder (repo) GitHub cloud service for hosting Git repos

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GitHub Git software for managing ﬁles in a folder (repo) GitHub cloud service for hosting Git repos

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Git software for managing ﬁles in a folder (repo)

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version control software Git software for managing ﬁles in a folder (repo)

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Git software for managing ﬁles in a folder (repo) version control software http://phdcomics.com/comics.php?f=1323 “I already have a system”

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rnaseq-analysis-update2-final.R rnaseq-analysis.R rnaseq-analysis-update.R rnaseq-analysis-update2.R rnaseq-analysis-update2-final-pkk.R “I already have a system” ad infinitum…

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rnaseq-analysis.R rnaseq-analysis.R rnaseq-analysis.R rnaseq-analysis.R rnaseq-analysis.R version control software “I already have a system” ad infinitum… rnaseq-analysis-update2-final.R rnaseq-analysis.R rnaseq-analysis-update.R rnaseq-analysis-update2.R rnaseq-analysis-update2-final-pkk.R

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version control software Git history of ﬁles is stored as a series of commits rnaseq-analysis.R rnaseq-analysis.R rnaseq-analysis.R rnaseq-analysis.R rnaseq-analysis.R

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version control software Git history of ﬁles is stored as a series of commits rnaseq-analysis.R

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version control software Git history of ﬁles is stored as a series of commits commit snapshot of ﬁle + useful message rnaseq-analysis.R

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version control software Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release rnaseq-analysis.R

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version control software Add new analysis Update analysis parameters Try new method Remove older results commit 6e40a27cb9415fd98fa3ef068efbb5e22eb7d497 Author: First Last Date: Sun Nov 18 11:10:25 2018 -0500 Clean up notes for release rnaseq-analysis.R

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rnaseq-analysis.R more commonly visualized horizontally Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release

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rnaseq-analysis.R checkout an older commit Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release

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rnaseq-analysis.R Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release inspect a diff between two commits

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rnaseq-analysis.R Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release commit best practices

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rnaseq-analysis.R Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release commit best practices 1. commits should be complete

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1. commits should be complete 2. commit messages should be meaningful commit best practices https://xkcd.com/1296/ https://chris.beams.io/posts/git-commit/

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Git version control software for managing ﬁles in a folder

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repo folder of ﬁles; a Git project Git version control software for managing ﬁles in a folder

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repo folder of files; a Git project commit snapshot of files in a repo Git version control software for managing files in a folder

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Git version control software for managing ﬁles in a folder git repo

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GitHub GitHub cloud service for hosting Git projects Git version control software for managing ﬁles in a folder git repo

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GitHub GitHub cloud service for hosting Git projects Git version control software for managing ﬁles in a folder git repo git repo

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GitHub git repo git repo GitHub: hosting service

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GitHub git repo git repo GitHub: hosting service sharing newest version

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GitHub git repo git repo GitHub: hosting service sharing git repo collaboration

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GitHub git repo git repo GitHub: hosting service sharing git repo collaboration

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GitHub?

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GitHub?

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GitHub?

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GitHub?

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GitHub?

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GitHub?

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why can’t we just use… Google Drive Dropbox …?

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GitHub is more than just a cloud

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GitHub is more than just a cloud sharing share the complete Git history

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GitHub is more than just a cloud sharing collaboration share the complete Git history open the code to suggestions and ﬁxes

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GitHub is more than just a cloud https://kbroman.org/github_tutorial/pages/why.html

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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GitHub was built for Git

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BitBucket GitLab GitHub GitHub isn’t the only option, but it’s a good one

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GitHub cloud service for hosting Git projects GitHub git repo git repo

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GitHub cloud service for hosting Git projects GitHub git repo git repo remote hosted copy of a repo local remote

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GitHub cloud service for hosting Git projects GitHub git repo git repo remote hosted copy of a repo local remote push/pull sync commits between local/remote push

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GitHub cloud service for hosting Git projects GitHub git repo git repo remote hosted copy of a repo local remote push/pull sync commits between local/remote pull push

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push/pull sync commits between local/remote GitHub cloud service for hosting Git projects GitHub git repo git repo git repo remote pull push local local remote hosted copy of a repo pull push

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repo folder of files; a Git project commit snapshot of files in a repo Git version control software for managing files in a folder

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repo folder of files; a Git project commit snapshot of files in a repo Git version control software for managing files in a folder GitHub cloud service for hosting Git projects remote remote copy of repo push/pull sync commits between local/remote

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awesome!

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https://xkcd.com/1597/ Git and GitHub IRL (in real life)

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Git is command line Git is unfriendly

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enough with the what, on to the how

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enough with the what, on to the how what you’ll need: 1.Git 2.GitHub account

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1.Git 2.GitHub account 3.Git GUI client enough with the what, on to the how what you’ll need:

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enough with the what, on to the how what you’ll need: 1.Git 2.GitHub account 3.Git GUI client GitHub Desktop GitKraken

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Git on the command line

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Git in RStudio

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Git in RStudio

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enough with the what, on to the how what you’ll need: 1.Git 2.GitHub account 3.Git GUI client 1. 2. 3. /username

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enough with the what, on to the how what you’ll need: 1.Git 2.GitHub account 3.Git GUI client link local/remote 1. 2. 3. /username

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enough with the what, on to the how

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pkimes$ git remote add origin https://github.com/pkimes/dfci-example.git pkimes$ git push -u origin master

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wait, I’m lost

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git repo local wait, I’m lost

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git repo local wait, I’m lost

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GitHub git repo local wait, I’m lost

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GitHub git repo git repo local remote wait, I’m lost

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GitHub git repo local remote link wait, I’m lost git repo

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GitHub git repo git repo local remote push wait, I’m lost

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awesome!

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wait, I’m still lost

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Alice Bartlett Senior Developer, Financial Times @alicebartlett Git for humans Git for humans https://speakerdeck.com/alicebartlett/git-for-humans

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happy Git and GitHub for the useR http://happygitwithr.com/

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introduction to data science (section VIII) https://rafalab.github.io/dsbook/

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data science course in a box https://github.com/rstudio-education/datascience-box

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let’s give it a try! https://rafalab.github.io/dsbook/ Sections 75 - 79