A Python course for Biologists

2009-07-05T00:00:00Z

These are the slides for a five-day course I gave at the Oxford Center for Gene function in April (on behalf of Nobleprog). It was the first teaching I’ve done, and it shows.

I should warn you that my Biology education ended at 16, and most of the examples in the slides came from what I could fathom from Wikipedia – needless to say I made plenty of mistakes. It’s all Creative Commons Attribution 2.0, so you have a lot of freedom to reuse the material if you want to. The slides where created using S5 and ReST, and the source is in the zip.

Building a Django App server on Vagrant

2010-12-29T00:00:00Z

Eric Holscher has recently written an excellent series of articles about provisioning an app server with chef. Around the same time, Gareth Rushgrove mentioned Vagrant - a tool that takes a lot of the pain out of managing development environments on virtual machines.

Stealing with both hands, I present the fewest commands necessary to get a Django app server running in a virtual machine.

Download & install virtualbox.
Install vagrant (should just be “gem install vagrant“)
vagrant box add lucid32 http://files.vagrantup.com/lucid32.box
git clone https://github.com/ericholscher/chef-django-example.git
cd chef-django-example
vagrant init
edit Vagrantfile

Add (or uncomment) these lines:


   config.vm.provisioner = :chef_solo
   config.chef.add_recipe "main"
   config.chef.json.merge!({
                            "run_list"=> [ "main::default", "main::python", "main::readthedocs" ],
                            "base_packages"=> ["git-core", "bash-completion"],
                            "users"=> {
                              "docs"=> {
                                "id"=> 1001,
                                "full_name"=> "Docs User",
                                "key"=> "ssh-rsa key-goes-here eric@Bahamut"
                              }
                            },
                            "groups"=> {
                              "docs"=> {
                                "gid"=> 201,
                                "members"=> ["docs"]
                              }
                            },
                            "ubuntu_python_packages" => ["python-setuptools", "python-pip", "python-dev", "libpq-dev"],
                            "pip_python_packages" => {
                              "virtualenv" => "1.5.1",
                              "mercurial" => "1.7"
                            },
                          }
                          )

edit cookbooks/main/recipies/default.rb


execute "apt-get update" do
  action :run
end

vagrant up

You now have an app server running the code for Readthedocs. You can’t do a lot with it as this server would need a database and a Celery server to talk to, but you can login and poke at the services:

$ vagrant ssh
vagrant@vagrantup:~$ pgrep gunicorn
vagrant@vagrantup:~$ sudo initctl list
vagrant@vagrantup:~$ sudo tail -f  /home/docs/sites/readthedocs.org/run/celery.log

You can’t resolve the names of Holscher’s other servers so you’ll see celery moaning in the logs.

It’s a shame that we don’t end up with a fully-working server to play with, but this still illustrates how easy vagrant and chef make it to build a server. It’s also not difficult to see how this config could be moved into another file in the repository and used to provision staging and production servers as well.

A brief explanation of what’s going on here:

When you run vagrant up Vagrant reads Vagrantfile, boots the VM then runs chef-solo to provision it (because you set config.vm.provisioner = :chef_solo). Chef follows the directions in cookbooks/main/recipies/default.rb to install the server (because we put the line config.chef.add_recipe "main" in Vagrantfile). When it’s executing, the data from config.chef.json is available in node - in Holscher’s examples this data is stored in the node.json file, though it’s called dna.js by vagrant (which seems to be a Chef convention).

Homebrewing PIL on Mac OSX

2010-02-14T00:00:00Z

Wrote my first homebrew formula. It builds PIL (with the optional jpeg, opentype, littleCMS dependencies). It’s a dupe (as it can be built from pip), and homebrew (reasonably enough) don’t want dups so I don’t expect anyone other than me will ever use it, but I should be able to find it again now.

Tom Dunham blog

A Python course for Biologists

Building a Django App server on Vagrant

A brief explanation of what’s going on here:

Homebrewing PIL on Mac OSX