Why of version control
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A short introduction to version control
Transcript of Why of version control
What is version controlAnnotated log of changes
Backup system
Collaboration tool
For any file type, but text files work best
Code!
A definitionVersion 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
Use case I: reviewer #3Paper submitted
After a couple of months Reviewer 3 writes:
“Please generate figure 3 with a higher resolution”
Use case I: reviewer #3Your 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
Use case I: reviewer #3How would version control have helped?
‘Turn back the clock’ to the code used
Rerun analysis
Recreate exact figure
Use case II
Use case IIFrom my own work:
$ cd scripts$ lsblat_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.plblat_parse3_backup.plblat_parse3.pl
Use case IIHow would version control have helped?
Older versions ‘hidden’ but still accessible
Annotated history of all changes available
Bonus:Allows for safely trying out changes
Annotated log of changes
http://starlogs.net/#lexnederbragt/denovo-assembly-tutorial
Use case III: collaborationExample: Wikipedia
http://en.wikipedia.org/wiki/Version_control
Fully traceable history of all contributions
Use case III: collaborationExample: Google docs
Fully traceable history of all contributions
Use case IV: how you workUsing version control:
makes me change code in small stepsmakes me log (annotate) my changes
makes me feel safe to change codemakes it easier to try out things
“But, this is way too complex!”
merge
tag
checkout
rebase
branch
pull request
conflict
https://www.atlassian.com/git/workflows
fetch
pull
pushdiff log
status
“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
Private versus public
Local, private git repo
Shared, central, private git repo
Shared, public git repo
My advice
Try git
See
http://software-carpentry.org/v5/novice/git/
