git introduction workshop for scientists
DESCRIPTION
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.TRANSCRIPT
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for me, for you.
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Git is version control.
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What is version control?
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The problem:
BackupsOrganizationCollaboration
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h!p://www.phdcomics.com/comics/archive.php?comicid=1531
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Thesis Thesis Thesis
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v1 v7-3v43_SN_comments_Sept_27_response
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Thesis_Final
Sept17_2013 Oct12_2013 Jan07_2014
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Manuscript
FinalVersion Nature_Sub ObscureJournal
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1
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1 2
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1 2
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1 2
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git commit -m "Initial commit."
the program
the git command
the command options git commit add checkout reset branch merge clone pull push
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Manuscript
manuscript.tex
Figure1.pdf
Figure2.pdf
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repository
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Outboxstaging area
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working copy
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Manuscript
git checkout …
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Outbox
manuscript.tex
• added 2 paragraphs• deleted 3 lines• moved 4 lines down• ...
git add …
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git commit …
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commit: 83296a31...author: Steven HamblinDate: Friday May 9, 20:03:39 2014
Fixed introduction in manuscript.tex
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Manuscript git checkout …
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manuscript.tex
• added 2 paragraphs• deleted 3 lines• moved 4 lines down• ...
git add …
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commit: 83296a31...author: Steven HamblinDate: Friday May 9, 20:03:39 2014
Fixed introduction in manuscript.texgit commit …
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Let’s try it.
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manuscript.tex
• added 2 paragraphs• deleted 3 lines• moved 4 lines down• ...
git add …
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git commit …
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commit: 83296a31...author: Steven HamblinDate: Friday May 9, 20:03:39 2014
Fixed introduction in manuscript.tex
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This is going to be an AWESOME NATURE PAPER!
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## README
This is the README for my AWESOME NATURE PAPER.
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git commit + git add
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commit: 83296a31...author: Steven HamblinDate: Friday May 9, 20:03:39 2014
Fixed introduction in manuscript.tex
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manuscript.tex
• added 2 paragraphs• deleted 3 lines• moved 4 lines down• ...
git commit -a —>
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Snapshot CSnapshot BSnapshot A
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Branching.
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PNAS
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HEAD
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Manuscript
master
PNAS
git checkout
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HEAD
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Exercise
Try this command: !
git log --graph --pretty --abbrev-commit
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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.
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Exercise
1. Now, checkout master again. 2. Merge the PNAS branch into
master again.
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Commit early, commit o!en!
Branch early, branch o!en!
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d0100
git reset git revert git diff
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git reset - - hard <commit>git reset - - so! <commit>
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git reset - - hard <commit>git reset - - so! <commit>
- -hard throws away changes, moves HEAD - -so! keeps changes, moves HEAD
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Exercise
1. Make changes and commit, twice. 2. Make uncommi#ed changes. 3. Use git reset to throw away the
uncommi#ed changes.
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Exercise
1. Make more uncommi#ed changes. 2. Use git reset to roll back the
repository without losing the uncommi!ed changes.
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git stash
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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.
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Collaboration
1 2
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user 1's local repository
user 2's local repository
user 1 user 2
remote repositorye.g. GitHub, Bitbucket
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git clone
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C1
Outbox
git push
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git pull
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git pullfe
tch
merge
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Exercise
1. Create a GitHub account (github.com)
2. Create a repository on GitHub. 3. Clone the repository to your
machine.
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Exercise
1. Make some local changes and commit them.
2. Push the changes to your remote repository.
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Exercise
1. Go to github.com and make some changes on the remote side.
2. Pull the changes into your local.
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Exercise
1. Advanced: change the same file locally and remotely to create a merge conflict.
2. Pull and resolve the conflict.
![Page 109: Git introduction workshop for scientists](https://reader034.vdocuments.us/reader034/viewer/2022051514/54835fd5b4af9f640d8b49ff/html5/thumbnails/109.jpg)
Exercise
1. Go to h#p://pco#le.github.io/learnGitBranching/
2. Do the “Main” Introduction sequence and the first “Remote” sequence.
![Page 110: Git introduction workshop for scientists](https://reader034.vdocuments.us/reader034/viewer/2022051514/54835fd5b4af9f640d8b49ff/html5/thumbnails/110.jpg)
Share and enjoy!