DFCI Introduction to Git and GitHub

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

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

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
2. why care about Git and GitHub?
3. why care about Git and GitHub? sharing collaboration version control
4. Git software for managing files in a folder (repo)
5. GitHub Git software for managing files in a folder (repo) GitHub cloud service for hosting Git repos
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)
7. GitHub Git software for managing files in a folder (repo) GitHub cloud service for hosting Git repos
8. GitHub Git software for managing files in a folder (repo) GitHub cloud service for hosting Git repos
9. Git software for managing files in a folder (repo)
10. version control software Git software for managing files in a folder (repo)
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”
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…
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
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
15. version control software Git history of files is stored as a series of commits rnaseq-analysis.R
16. version control software Git history of files is stored as a series of commits commit snapshot of file + useful message rnaseq-analysis.R
17. version control software Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release rnaseq-analysis.R
18. version control software Add new analysis Update analysis parameters Try new method Remove older results commit 6e40a27cb9415fd98fa3ef068efbb5e22eb7d497 Author: First Last <myemail@mydomain.com> Date: Sun Nov 18 11:10:25 2018 -0500 Clean up notes for release rnaseq-analysis.R
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
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
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
22. rnaseq-analysis.R Add new analysis Update analysis parameters Try new method Remove older results Clean up notes for release commit best practices
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
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/
25. Git version control software for managing files in a folder
26. repo folder of files; a Git project Git version control software for managing files in a folder
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
28. Git version control software for managing files in a folder git repo
29. GitHub GitHub cloud service for hosting Git projects Git version control software for managing files in a folder git repo
30. GitHub GitHub cloud service for hosting Git projects Git version control software for managing files in a folder git repo git repo
31. GitHub git repo git repo GitHub: hosting service
32. GitHub git repo git repo GitHub: hosting service sharing newest version
33. GitHub git repo git repo GitHub: hosting service sharing git repo collaboration
34. GitHub git repo git repo GitHub: hosting service sharing git repo collaboration
35. GitHub?
36. GitHub?
37. GitHub?
38. GitHub?
39. GitHub?
40. GitHub?
41. why can’t we just use… Google Drive Dropbox …?
42. GitHub is more than just a cloud
43. GitHub is more than just a cloud sharing share the complete Git history
44. GitHub is more than just a cloud sharing collaboration share the complete Git history open the code to suggestions and fixes
45. GitHub is more than just a cloud https://kbroman.org/github_tutorial/pages/why.html
46. GitHub was built for Git
47. GitHub was built for Git
48. GitHub was built for Git
49. GitHub was built for Git
50. GitHub was built for Git
51. GitHub was built for Git
52. GitHub was built for Git
53. GitHub was built for Git
54. GitHub was built for Git
55. BitBucket GitLab GitHub GitHub isn’t the only option, but it’s a good one
56. GitHub cloud service for hosting Git projects GitHub git repo git repo
57. GitHub cloud service for hosting Git projects GitHub git repo git repo remote hosted copy of a repo local remote
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
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
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
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
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
63. awesome!
64. https://xkcd.com/1597/ Git and GitHub IRL (in real life)
65. Git is command line Git is unfriendly
66. enough with the what, on to the how
67. enough with the what, on to the how what you’ll need: 1.Git 2.GitHub account
68. 1.Git 2.GitHub account 3.Git GUI client enough with the what, on to the how what you’ll need:
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
70. Git on the command line
71. Git in RStudio
72. Git in RStudio
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
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
75. enough with the what, on to the how
92. pkimes$ git remote add origin https://github.com/pkimes/dfci-example.git pkimes$ git push -u origin master
97. wait, I’m lost
98. git repo local wait, I’m lost
99. git repo local wait, I’m lost
100. GitHub git repo local wait, I’m lost
101. GitHub git repo git repo local remote wait, I’m lost
102. GitHub git repo local remote link wait, I’m lost git repo
103. GitHub git repo git repo local remote push wait, I’m lost
104. awesome!
105. wait, I’m still lost
106. Alice Bartlett Senior Developer, Financial Times @alicebartlett Git for humans Git for humans https://speakerdeck.com/alicebartlett/git-for-humans
107. happy Git and GitHub for the useR http://happygitwithr.com/
108. introduction to data science (section VIII) https://rafalab.github.io/dsbook/
109. data science course in a box https://github.com/rstudio-education/datascience-box
110. let’s give it a try! https://rafalab.github.io/dsbook/ Sections 75 - 79