[Biopython-dev] Reproducible Biopython VM images

Christian Brueffer christian at brueffer.de
Tue Mar 17 11:34:24 UTC 2015

Hi everyone,

for development, testing, and release engineering, it would be nice to 
have a comprehensive VM image that has all dependencies, and tools we 
have wrappers for already installed.  Even better if it's easy to 
re-create by anyone!

I've started working on this based on Vagrant 
(https://www.vagrantup.com/).  My current (minimal) work is in the "vm" 
branch at https://github.com/cbrueffer/biopython ; it consists the two 
added files Vagrantfile and vmbootstrap.sh.

A VM can be created by first installing Vagrant and a supported VM 
software (e.g., Virtualbox). Then:

git clone -b vm https://git@github.com/cbrueffer/biopython.git
cd biopython
vagrant up  # downloads the base OS image and executes vmbootstrap.sh
vagrant ssh  # SSH access to the VM

The vmbootstrap.sh script currently installs an (incomplete) set of 
dependencies, installs the checked out Biopython version and runs the 
tests in offline mode.  Some tests still fail due to the aforementioned 
(currently) unmet dependencies.

The directory from which "vagrant up" was called (in this case the 
repository root) is available as /vagrant from within the VM.

Feedback welcome!



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