Using GitHub for scientific research Jon W. Carr Language Evolution - - PowerPoint PPT Presentation

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Using GitHub for scientific research Jon W. Carr Language Evolution - - PowerPoint PPT Presentation

Jan 11, 2024 733 likes •1.04k views

Using GitHub for scientific research Jon W. Carr Language Evolution and Computation Research Unit School of Philosophy, Psychology and Language Sciences University of Edinburgh Three good reasons to use GitHub Version control Share and

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Jon W. Carr Language Evolution and Computation Research Unit School of Philosophy, Psychology and Language Sciences University of Edinburgh

Using GitHub for scientific research

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Version control Share and collaborate Publish your work

Three good reasons to use GitHub

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collaborator

clone

github pages

commit

repository

merge

branch

pull request

master

.gitignore git

SHA hash

sync

command line tools

issues

blame

history

atom

public

private

markdown

wiki

gist

fork

release

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Background Specifics Demonstration Collaborative project

Today’s workshop

Quiz

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GitHub Education

Free micro account for students Host 5 private repositories Usually $7 per month

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Big picture

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Repository

Key terms

Branch Fork Commit Pull request

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Repository

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Commit

1 def Hello(name):
 2 greeting = "Hello " + name
 3 print greeting

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Commit

1 def Hello(name):
 2 greeting = "Hello " + name
 3 print greeting 4 5 def Bye(name): 6 valediction = "Bye bye " + name 7 print valediction

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def Raise(x, y):
 z = x ** y return z def Square(x):
 y = Raise(x, 2) return y def Cube(x):
 y = Raise(x, 3) return y

Revert a commit

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def Raise(x, y):
 z = x ** y return z def Square(x):
 y = Raise(x, 2) return y def Cube(x):
 y = Raise(x, 3) return y def Square(x):
 y = Raise(x, 2) return y

Revert a commit

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def Raise(x, y):
 z = x ** y return z def Square(x):
 y = Raise(x, 2) return y def Cube(x):
 y = Raise(x, 3) return y

Roll back to a previous commit

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def Raise(x, y):
 z = x ** y return z def Square(x):
 y = Raise(x, 2) return y

Roll back to a previous commit

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Repo Branch 1 Branch 2 Branch 3

Branch

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GitHub Main public repo Public forks

Fork

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Pull request

Pull request

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GitHub Atom

Two handy apps

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GitHub

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Atom

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.gitignore

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(GitHub Flavored) Markdown

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Other GitHub features

Issues: Bug reporting and feature requests Wiki: Document the project Pages: Free webpage for your project Gist: A mini repo for snippets of text

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Demo…

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Collaborative project

Aim: Build a simple Mantel Test module in Python Three teams will each implement part of the code Then we’ll test our code at the end

Team 1

ReadFile()

Team 2

PairwiseDistances()

Team 3

MonteCarlo()

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Quiz

  • 1. What’s the name of the GitHub mascot?
  • 2. What’s the difference between a fork and a branch?
  • 3. What’s a pull request?
  • 4. Can you delete a previous commit?
  • 5. What would you use a .gitignore file for?
  • 6. What could you use GitHub Issues for?
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Homework

Merge the functions created by the other two teams into your fork of the repository Test out the final code for yourself! (if you’re keen)