PyCharm, Vagrant, Fabric & Anaconda

Installing the whole development toolchain for Colour roughly means deploying:

I decided to see how I could make that setup a bit more portable and easier to deploy.

That's where Vagrant kicks in along PyCharm and Anaconda!

The following guide assume that you have that you have PyCharm installed and are using Mac Os X, although it should pretty much be platform agnostic.

Development Workspace Creation

  • On your local filesystem, in your development workspace, create a directory colour-science and cd into it:
mkdir colour-science
cd colour-science
git clone git://
  • You should now have a colour-vagrant directory nested into the colour-science one.

    Let's open the colour-vagrant directory into PyCharm.

Vagrant Installation

We will loosely follow Jetbrain's PyCharm Documentation.

  • Install VirtualBox.

  • Install Vagrant.

  • Install Fabric, this is the provider needed for the colour-vagrant environment:

    pip install fabric

    Initially, I was provisioning with Puppet. It was cumbersome to use, so I decided to go for Fabric and the fabric-vagrant plugin.

  • Install XQuartz: This is the X11 display server for Mac Os X. The virtual machine will export the display to it so that you can see the figures from Matplotlib.

  • VirtualBox directories syncing performance degrades quickly with large number of files.

    As a result the directories syncing is done with NFS.

    You will however be asked for your Mac Os X password at each virtual machine spin up because Vagrant needs to modify configuration files on the Mac Os X host.

    In order to avoid that and following the Vagrant Documentation, you can edit your Mac Os X /etc/sudoers file and append the following content:

    Cmnd_Alias VAGRANT_EXPORTS_ADD = /usr/bin/tee -a /etc/exports
    Cmnd_Alias VAGRANT_NFSD = /sbin/nfsd restart
    Cmnd_Alias VAGRANT_EXPORTS_REMOVE = /usr/bin/sed -E -e /*/ d -ibak /etc/exports

PyCharm Vagrant Configuration

The canonical way is to use Vagrant from the command line as described in Vagrant Documentation, but here we will leverage the PyCharm integration.

Your configuration screen should be approximately as follows:


Vagrant Up

With everything setup, hit the PyCharm ---> Tools ---> Vagrant ---> Up menu item to spin up the virtual machine.

You can go grab a coffee, the initial provisioning will take roughly 25-30 minutes.

If the provisioning ended smoothly, you should have the following elements available:

  • colour, colour-notebooks and repositories cloned into the colour-science directory right next to the colour-vagrant one.
  • Remote Python environments installed into the virtual machine at the following location with all the dependencies needed:
vagrant@precise64:~$ cd /home/vagrant/anaconda/envs/
vagrant@precise64:~/anaconda/envs$ ll
total 20
drwxrwxr-x  5 vagrant vagrant 4096 Sep  5 10:00 ./
drwxrwxr-x 14 vagrant vagrant 4096 Sep  5 10:00 ../
drwxrwxr-x 12 vagrant vagrant 4096 Sep  5 10:00 python2.7/
drwxrwxr-x 11 vagrant vagrant 4096 Sep  5 09:58 python3.5/
  • The website served from the virtual machine at the following address: http://localhost:8080/

PyCharm Environment Configuration

  • Add the various remote Python interpreters to PyCharm following the quickstart guide: Remote interpreter via virtual box: 2

    The remote Python interpreters paths are as follows:

    • /home/vagrant/anaconda/envs/python2.7/bin/python
    • /home/vagrant/anaconda/envs/python3.5/bin/python
  • Add the paths mappings from the Mac Os X host to the virtual machine in the Defaults configurations, in my case the mappings are as follows:

    /Users/KelSolaar/Documents/Developement/colour-science = /colour-science

Your Run/Debug configuration screen should be approximately looking like that:



SSH Connection & Display

Accessing the virtual machine is done by using PyCharm ---> Tools Start SSH session... menu item.

However if you want to be able to export the display and see the figures you will have to manually ssh into the virtual machine:

ssh -Y vagrant@

Password is vagrant.

You will also need to add the virtual machine to the X11 hosts by issuing the following command on the Mac Os X host:

xhost +

Jupyter Notebooks

The Jupyter Notebooks server is started as follows:

cd /colour-science/colour-notebooks/notebooks
ipython notebook --pylab=inline --ip=

Then you can access it on the Mac Os X host at the following url: http://localhost:8888/

Remote Python Environments & Interpreters

You can activate the remote Python environments in the virtual machine by issuing those commands:

For python2.7:

source activate python2.7

For python3.5:

source activate python3.5


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