A short introduction to version control

1. Version control
What?
Why?
How?
Lex Nederbragt, lex.nederbragt@ibv.uio.no

2. What is version control
Annotated log of changes
Backup system
Collaboration tool
For any file type, but text files work best
Code!

3. A definition
Version control
A tool for managing changes to a set of files
Each set of changes creates a new revision of the files
Allows users to recover old revisions reliably
Helps manage conflicting changes made by different users
From the Software Carpentry website

4. Use case I: reviewer #3
Paper submitted
After a couple of months Reviewer 3 writes:
“Please generate figure 3 with a higher resolution”

5. Use case I: reviewer #3
Your reply to the reviewer
We have continued to work on the code that
had generated the figures for the original
paper, and couldn’t recreate the exact code used
Our new code generates a graph which slightly
alters the interpretation

6. Use case I: reviewer #3
How would version control have helped?
‘Turn back the clock’ to the code used
Rerun analysis
Recreate exact figure

7. Use case II

8. Use case II
From my own work:
$ cd scripts
$ ls
blat_parse4.pl old_versions snps_flanks_2_fastq.pl
$ ls old_versions/
blat_parse2.pl blat_parse_attemp1.pl blat_parse.pl.bak
blat_parse.pl
blat_parse3_backup.pl
blat_parse3.pl

9. Use case II
How would version control have helped?
Older versions ‘hidden’ but still accessible
Annotated history of all changes available
Bonus:
Allows for safely trying out changes

10. Annotated log of changes
http://starlogs.net/#lexnederbragt/denovo-assembly-tutorial

11. Use case III: collaboration
Example: Wikipedia
http://en.wikipedia.org/wiki/Version_control
Fully traceable history of all contributions

12. Use case III: collaboration
Example: Google docs
Fully traceable history of all contributions

13. Use case IV: how you work
Using version control:
makes me change code in small steps
makes me log (annotate) my changes
makes me feel safe to change code
makes it easier to try out things

14. “But, this is way too complex!”
merge
tag
checkout
rebase
branch
pull request
conflict
https://www.atlassian.com/git/workflows
fetch
pull
push
diff log
status

15. “But, this is way too complex!”
Can keep it very simple
Just one piece of code, only you work on it
…
A few scripts in one folder, made available online
A large code base with multiple contributors

16. Private versus public
Local, private git repo
Shared, central, private git repo
Shared, public git repo

17. My advice
Try git
See
http://software-carpentry.org/v5/novice/git/