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Git introduction workshop for scientists

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Steven Hamblin
Steven Hamblin

These are the slides for a workshop I gave on June 2, 2014 at USC. They are an introduction to git and version control for my fellow scientists. Note that the branching section draws heavily on the diagrams and material from the Pro Git book (http://git-scm.com/book/), though I reimplemented them for my own uses.

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for me, for you.
Git is version control.
What is version control?
The problem: Backups Organization Collaboration
h p://www.phdcomics.com/comics/archive.php?comicid=1531
Thesis Thesis Thesis
v1 v7-3 v43_SN_ comments_ Sept_27_ response
Thesis_Final Sept17_2013 Oct12_2013 Jan07_2014
Manuscript FinalVersion Nature_Sub ObscureJournal
1
1 2
1 2
1 2
git commit -m "Initial commit." the program the git command the command options git commit add checkout reset branch merge clone pull push
Manuscript manuscript.tex Figure1.pdf Figure2.pdf
repository
Outbox staging area
working copy
Manuscript git checkout …
Outbox manuscript.tex • added 2 paragraphs • deleted 3 lines • moved 4 lines down • ... git add …
git commit … Outbox commit: 83296a31... author: Steven Hamblin Date: Friday May 9, 20:03:39 2014 Fixed introduction in manuscript.tex
Manuscript git checkout … Outbox manuscript.tex • added 2 paragraphs • deleted 3 lines • moved 4 lines down • ... git add … Outbox commit: 83296a31... author: Steven Hamblin Date: Friday May 9, 20:03:39 2014 Fixed introduction in manuscript.tex git commit …
Let’s try it.
Outbox manuscript.tex • added 2 paragraphs • deleted 3 lines • moved 4 lines down • ... git add …
git commit … Outbox commit: 83296a31... author: Steven Hamblin Date: Friday May 9, 20:03:39 2014 Fixed introduction in manuscript.tex
commit size tree author committer 09f0e... Steven Steven Initial commit. tree size blob blob blob 25351 manuscript.txt README.md 3a44f 8762e Figure1.pdf blob size This is going to be an AWESOME NATURE PAPER! blob size ... binary data ... blob size ## README This is the README for my AWESOME NATURE PAPER. de102... 09f0e... 25351... 3a44f... 8762e...
git commit + git add Outbox commit: 83296a31... author: Steven Hamblin Date: Friday May 9, 20:03:39 2014 Fixed introduction in manuscript.tex Outbox manuscript.tex • added 2 paragraphs • deleted 3 lines • moved 4 lines down • ... git commit -a —>
commit size tree author committer 09f0e... Steven Steven Initial commit. de102... commit size tree author committer 47ae6... Steven Steven Added my plan d0100... c315c... parent de102... commit size tree author committer 7cae3... Steven Steven Added note of caution. parent c315c... Snapshot CSnapshot BSnapshot A
Branching.
Snapshot CSnapshot BSnapshot A de102 d0100 c315c master
de102 d0100 c315c master PNAS
de102 d0100 c315c master PNAS HEAD
Manuscript master PNAS git checkout
de102 d0100 c315c master PNAS HEAD
de102 d0100 c315c master PNAS HEAD fc547
de102 d0100 c315c master PNAS HEAD fc547
de102 d0100 c315c master PNAS HEAD fc547 b755a
de102 d0100 c315c master PNAS HEAD fc547 b755a 20bb1
Exercise Try this command: ! git log --graph --pretty --abbrev-commit
Exercise 1. Checkout the PNAS branch again. 2. Create a new file with some references in it. Call it refs.txt. 3. Add the file, then commit it.
Exercise 1. Now, checkout master again. 2. Merge the PNAS branch into master again.
Commit early, commit o en! Branch early, branch o en!
d0100 git reset git revert git diff
git reset - - hard <commit> git reset - - so <commit>
git reset - - hard <commit> git reset - - so <commit> - -hard throws away changes, moves HEAD - -so keeps changes, moves HEAD
de102 d0100 c315c master HEAD b755a
de102 d0100 c315c master HEAD deleted
Exercise 1. Make changes and commit, twice. 2. Make uncommi ed changes. 3. Use git reset to throw away the uncommi ed changes.
Exercise 1. Make more uncommi ed changes. 2. Use git reset to roll back the repository without losing the uncommi ed changes.
git stash
Exercise 1. Make uncommi ed changes. 2. Stash those changes 3. Switch branches. Make changes and commit. 4. Switch back and retrieve your stashed changes.
Collaboration
user 1's local repository user 2's local repository user 1 user 2 remote repository e.g. GitHub, Bitbucket
git clone
C1 Outbox git push
git pull
git pullfetch merge
Exercise 1. Create a GitHub account (github.com) 2. Create a repository on GitHub. 3. Clone the repository to your machine.
Exercise 1. Make some local changes and commit them. 2. Push the changes to your remote repository.
Exercise 1. Go to github.com and make some changes on the remote side. 2. Pull the changes into your local.
Exercise 1. Advanced: change the same file locally and remotely to create a merge conflict. 2. Pull and resolve the conflict.
Exercise 1. Go to h p://pco le.github.io/ learnGitBranching/ 2. Do the “Main” Introduction sequence and the first “Remote” sequence.
Share and enjoy!
Steven Hamblin (steven.hamblin@gmail.com) h p://winawer.org

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