DFCI Introduction to Git and GitHub

Data Science Seminar
Department of Data Sciences
Dana-Farber Cancer Institute

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Transcript

1. 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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2. why care about
   Git and GitHub?
   

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3. why care about
   Git and GitHub?
   sharing
   collaboration
   version control
   

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4. Git
   software for managing
   files in a folder (repo)
   

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

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

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

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9. Git
   software for managing
   files in a folder (repo)
   

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

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11. 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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12. 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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13. 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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14. 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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15. version control software
    Git
    history of files is stored
    as a series of commits
    rnaseq-analysis.R
    

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16. 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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17. 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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18. 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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19. 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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20. 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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21. 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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22. 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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23. 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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24. 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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25. Git
    version control software for
    managing files in a folder
    

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

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

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

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30. 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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31. GitHub
    git repo
    git repo
    GitHub: hosting service
    

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

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

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

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35. GitHub?
    

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36. GitHub?
    

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37. GitHub?
    

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38. GitHub?
    

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39. GitHub?
    

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40. GitHub?
    

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

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42. GitHub is more than just a cloud
    

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

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

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46. GitHub was built for Git
    

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47. GitHub was built for Git
    

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48. GitHub was built for Git
    

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49. GitHub was built for Git
    

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50. GitHub was built for Git
    

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51. GitHub was built for Git
    

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52. GitHub was built for Git
    

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53. GitHub was built for Git
    

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54. GitHub was built for Git
    

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

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

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

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58. 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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59. 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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60. 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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61. 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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62. 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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63. awesome!
    

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

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65. Git is
    command line
    Git is unfriendly
    

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66. enough with the what,
    on to the how
    

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

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68. 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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69. 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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70. Git on the
    command line
    

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71. Git in RStudio
    

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72. Git in RStudio
    

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73. 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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74. 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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75. enough with the what,
    on to the how
    

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

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97. wait, I’m lost
    

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98. git repo
    local
    wait, I’m lost
    

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99. git repo
    local
    wait, I’m lost
    

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100. GitHub
     git repo
     local
     wait, I’m lost
     

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

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

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

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104. awesome!
     

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105. wait, I’m still lost
     

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

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

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

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

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

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