Getting a scientific python install up and running is still way too complicated. In this post I describe how I use a conda to keep a reproducible record of the packages I use.

In the past, I have usually hacked together my own developing environment through whatever tools were most convenient (pip, github clones, built-in packages from expansive standard python distros). This is a workable solution if you’re only doing it once, but it can be quite challenge to achieve the exact same python environment on a new machine. This is annoying in lots of contexts, but it’s especially problematic for scientific computing because it means others (or even your future self) may not be able to reproduce your published results.

My solution to this issue is to use Conda, which forms an independent part of the Anaconda python distro (I use the lighter mini-conda). At its core, Conda is a package manager which tries to be smart about managing your python environment. There are many competitors in this area (the classic solution is pip combined with virtualenv, brew and macports are other possibilities), but Conda has a few useful features that collectively make it preferable for scientific computing:

  • Conda packages are distributed in compiled form, which avoids all build-related issues (e.g., missing dependencies, broken compilers, weird build environments). If the package has been built properly, it is literally plug and play. For a taste of how smoothly this works with complex packages, try conda install mayavi compared to brew install mayavi and see what you get.
  • If a conda package is not available, it is surprisingly easy to build one from python libraries. Most pip packages can be built for conda with two commands: conda skeleton pypi [pip package] followed by conda build [pip package]. Adapting github repos requires a bit more manual editing of a YAML file but even this is simple enough (see e.g. this pycortex recipe I wrote). Under the hood, there’s quite a bit of cleverness going on with e.g. converting absolute paths to relative to enable this to work as smoothly as it does.
  • Conda includes a free package repository at anaconda.org, where users can upload packages. At build time, users are nudged toward setting anaconda_upload: yes in their .condarc files, which means that any successful build is uploaded to your anaconda.org repo. This option appears to be popular because a huge number of user-built packages are available here. This is useful for quickly checking out more obscure packages that aren’t in the official conda channel.
  • That being said, for reproducibility it is probably a better idea to build packages yourself and upload them to your own repository since other users can otherwise break your dependencies by removing or altering the package you’re channeling. Uploading your own builds has the added advantage of solving your deployment issues — all you have to do on a new machine is add your repository to the set conda will search when installing packages (e.g., conda config --add channels jcarlin), and the standard conda install command will just work.
  • Conda’s environment handling is quite good, and seems to err on the side of safety at the expense of disk space (ie, copy everything) compared to e.g. brew. I have yet to bump into any interactions between different environments. Generally, it’s a good idea to have a different environment for each broad task you use python for (I use one for psychopy, one for neuroimaging analysis and one for web development), since packages sometimes require different versions of the same modules. Conda tries to manage such situations, but often the compromise is to downgrade core packages (e.g. numpy) to fairly old versions.

In summary, my entire python environment is now made up of Conda packages, which is neat because it means that I can reproduce my python setup anywhere. There is a bit of overhead in going this route (especially if you want to avoid having dependencies from other anaconda.org users), but this should be recouped quickly down the road as the code gets deployed to psychophysics test laptops, cloud compute, other lab members…


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