Introduction to version control, lecture at the "Programming for Evolutionary Biology" workshop in Leipzig 2013

1. Git & version control

2. What is version control?
● A way to:
– Keep a log of all the changes made to your scripts
& data
– Synchronize all the copies of your scripts in all
your computers
– Be able to go back to previous working versions

3. Version control - example
● A project on which I
am working on at the
moment (Genotype
Space)
● Started working on
April 2012
● ~2,000 revisions

4. Version control – how does it work?
● Every time I make significant changes to a
script, or get new results, I save a new
“revision”
● Each revision is associated to a description,
and a date

5. Example log

6. Advantages of version control
● What was the version of my scripts when I
generated the results included in the paper, 2
years ago?

7. Advantages of version control
● What was the version of my scripts when I
generated the results included in the paper, 2
years ago?
● I've accidentally removed a portion of my
code. Can I go back?

8. Advantages of version control
● What was the version of my scripts when I
generated the results included in the paper, 2
years ago?
● I've accidentally removed a portion of my
code. Can I go back?
● I've found a folder containing scripts and
results. Are the scripts updated to the latest
version?

9. Git and Version control
● A popular software for version control is “git”
● Used for the Linux kernel
● Adopted by http://github.com, popular hosting
website for open source projects

10. How to get git?
● http://git-scm.com/
● Linux: apt-get install git

11. How to get git?
● http://git-scm.com/
● Linux: apt-get install git
● Windows, Mac, Linux: you can install
“tortoise-hg”, an
– http://tortoisehg.bitbucket.org/

12. Definition: the repository
● The repository is the folder where all the
scripts (and eventually results) of a project are
stored

13. Example of repository: bedtools

14. Examples of repository: github

15. Example of repository: database
lecture

16. How to create a repository
(on your computer)
● Connect to evopcompute
● Create a folder
● “cd” to it
● Type git init

17. git init
● The command git init creates a new repository
in the current folder
● All the files and subfolder will be included in
the repo (although you will have to add them
manually)

18. git clone
● Alternatively, you can “clone” an existing
repository
● git clone <url-to-repository>

19. git add
● Let's add a new file to the repository
● First, let's create a file:
– gedit README.txt
● Now, let's tell git to track it:
– git add README.txt

20. Effects of git add
● The command git add tells git that you want to
keep track of all the changes of that file

21. git commit
● Let's save our first revision:
– git commit README.txt -m “DOCS: added a
readme”

22. git commit
● Let's save our first revision:
– git commit README.txt -m “DOCS: added a
readme”
● Explanation:
– git commit → create a new commit
– README.txt → the new commit refers only to the
file README.txt
– -m “....” → description of the commit

23. git log
● Let's see our new commit:
– git log

24. Let's modify our file: git diff
● The command git diff tells you all the changes
made since the last commit
● Let's modify our README.txt file, and see how
the changes are tracked
– echo “new line after first commit” > README.txt
– git diff

25. Let's make more commits
– echo “new line after first commit” > README.txt
– git diff
– git commit -m “DOCS: added a new line”
– echo “another new line after first commit” >
README.txt
– git commit -m “DOCS: added another new line”
– git log

26. git revert
● If we don't like some new changes, we can
revert them:
– git log
– git revert <id of the revision>

27. Syncronyzing a repository with
github / bitbucket
● A common practice is to have multiple copies
of your code, stored in different places
● Github and bitbucket are two free hosting
services for code
● Bitbucket offers unlimited space hosting, so
you can keep a backup of your code there

28. How to synchronize your repo with
github
● Create an account at http://github.com
● Follow the instructions on setting up a ssh key
– https://help.github.com/articles/set-up-git
– https://help.github.com/articles/generating-ssh-key
s
● Create a new repository from the web
interface

29. git pull & push
● gt clone → download a repository from
github/bitbucket, for the first time
● git pull → download the latest changes from
your repository (e.g. github/bitbucket), and
update the code on your computer
● git push → upload all the latest changes to the
remote repo

30. Git pull & push – best practices
● Always download the latest changes (git pull)
before uploading new ones (git push)
● Otherwise, you will have some version
conflicts
● Never force a git push

31. How to collaborate on
github/bitbucket
● Let's imagine we want to contribute to
biopython:

32. How to collaborate on
github/bitbucket
● To contribute to a open source repository on
github/bitbucket, we will have to:
– “fork” the repository using the web interface
– Make changes to our forked repository
– Send a “pull request” to the original repository
once ready

33. Fork repository

34. Forked Repository

35. Contributing to biopython
map of repositories
Official BioPython repo Fork of BioPython on your
on github.com FORK account on github.com
PULL
REQUEST
CLONE
Local copy of your
BioPython fork, on your
computer

36. Contributing to biopython
● Make your changes on your local computer,
and upload them to your forked repository on
github
● When your changes are ready for biopython,
do a “Pull request”

37. Contributing to biopython

38. Pull Request

39. Pull Request

40. Version control - resume
● Version control is a good practice to keep a
log of all the changes in your code
● Many bioinformatics tools are developed
under version control

41. Having fun with stats
(my Genotype Space project)

42. Having fun with stats
(my Genotype Space project)
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