.py in the sky

Musings on Python, Astronomy, and Open Science

What Python installations are scientists using?

Back in November 2012, I asked Python users in Science to fill out a survey to find out what Python, Numpy, and Scipy versions they were using, and how they maintain their installation. My motivation for this was to collect quantitative information to inform discussions amongst developers regarding which versions to support, because those discussions are usually based only on guessing and personal experience. In particular, there has been some discussion in the Astropy project regarding whether we should drop support for Numpy 1.4, but we had no quantitative information about whether this would affect many users (which motivated this study).

In this post, I'll give an overview of the results, as well as access to the (anonymized) raw data. First, I should mention that given my area of research and networks, the only community I obtained significant data are Astronomers, so the results I present here only include these (though I also provide the raw data for the remaining users for anyone interested).

Before I show the results, I just want to make it clear that I am not claiming that the results are a true sampling of Python user levels. I advertised the poll via Twitter, a couple of Python mailing lists, and the Facebook group for Astronomers. The survey was announced on different days on Twitter and Facebook, so there may be some useful information about the typical Python installations of Twitter vs Facebook users buried in the data that I won't cover here. If anyone is interested about when the announcements were made, to correlate with response peaks in the data, please let me know!

With that out of the way... let's look at the results!


First, some general stats - there were 313 responses in total, of which 244 were related to Astronomy (where I use the term in the broadest sense, including solar physics, planetary science, astrophysics, and cosmology). The responses were recorded between November 17th 2012 and December 2nd 2012 (at which point the rate of responses had gone down to less than one a day).

Python Versions

python versions

As shown above, an overwhelming 80% of Astronomers use Python 2.7, and almost 15% use Python 2.6. Almost no-one uses Python 3.x for production work yet, which is not surprising, given that at the time of the poll there were not stable versions for all the crucial packages in a scientific Python stack (in particular, Matplotlib only released their first Python 3.x compatible release in December). It will be interesting to see how this fraction changes over the next year (more on that in future blog posts).

Numpy Versions

python versions

In the above plot, dev includes anything that is a developer version more recent than the 1.6.2 release (which was the latest stable release at the time of the poll). The distribution is again significantly peaked, with almost 80% of respondents using Numpy 1.6.x. There is more of a spread in the remaining versions compared with the Python versions, but the vast majority of people are using Numpy 1.5.x or more recent.

Scipy Versions

python versions

In the above plot, dev includes anything that is a developer version more recent than the stable 0.11 release (which was the latest stable release at the time of the poll). Unlike the Python and Numpy versions, which are almost exclusively dominated by two versions, the Scipy versions show a larger spread, with the most popular version, 0.10.x, representing less than 45% of users.

I originally thought that Scipy released more often than Numpy, and this would explain the difference, but it seems that both projects have been releasing at a reasonably similar rate (see here and here). Therefore, this might be to do with package managers, or simply to the fact that Numpy is used more often than Scipy, and users are therefore more likely to run into bugs and update to the latest stable version? I have to admit that I would not even be able to tell without checking what Scipy version I am using, whereas I know I'm using Numpy 1.6.2 for production work.


We now get to some very interesting statistics - how users install Python and dependencies. While Python is awesome in many respects, installation is probably the biggest hurdle that users have to jump to get started.

python versions

I'm not sure if anyone's quantitatively looked at this before, but this was the first time that I really got a sense for all the different ways that one can maintain a Python installation, and which methods are the most popular. The options shown above are described below:

Linux Manager means linux package managers (apt-get, yum, etc.) Source means an installation from the source code. This means either downloading the source code and running python setup.py install, or using pip install or easy_install. EPD stands for the Enthought Python Distribution, which is a scientific Python bundle that includes e.g. Numpy, Scipy, Matplotlib, and many other packages. It is free for users at academic institutions. MacPorts is one of the most widely used package managers on Mac, and I have provided instructions for getting set up with Python and MacPorts here. Official Installers refers to the MacOS X disk images, Linux RPMs, and Windows installers that are provided by some projects (including Python itself, Numpy, and Scipy). Admins means that Python and the packages were installed by System Administrators. SciSoft and STScI Python are two Astronomy-specific software bundles. And ActivePython is similar to EPD, but where binary packages are downloaded on-the-fly as needed.

Of course, some of these are not orthogonal, because for example easy_install can be used to install additional packages not in EPD. But the responses from the survey refer to how the main packages (Python, Numpy, and Scipy) were installed.

What can we take away from the results?

  • If we combine the Linux Package Managers and MacPorts (one of the Mac Package Managers) into a more general Package Managers category, this amounts to around 40% of users, the single largest group.

  • Only a small fraction of people use the official binary installers, with many more people installing from source. This was surprising to me, given how quick/easy it is to install Python, Numpy, Scipy, and Matplotlib using the official installers. I think this is down to the fact that this is not a well-documented installation procedure, and is platform dependent.

  • Astronomy-specific bundles (SciSoft and STScI Python) are not as widely used, which indicates that more effort should be put in getting packages in existing package managers than building new software bundles.

  • A small fraction (around 7%) have no idea how they installed Python and other packages, so they may run into issues when they try and upgrade in future. If you install Python for someone, please explain to them what you are doing and how they can update packages in future!

I personally feel that we should encourage users to install Python and whatever dependencies are available from package managers. Of course, in some cases users don't have root access, but this generally means that they have sysadmins, so in those cases, the best option is still for the sysadmins to install the main Python packages via package managers.


To me, one of the most interesting results is that a large number of people have a reasonably up-to-date installation, with Python 2.7 and Numpy 1.6.x, and I imagine that the Python 2.7 peak is here to stay, given that the transition to Python 3 will be slow.

For developers, supporting only Python 2.6 and above seems like a sensible choice at this stage (a decision we made within Astropy), and given the imminent release of Numpy 1.7.0, I think that developers can start thinking about dropping support for Numpy 1.4 in the near future. For Scipy, things are a little more difficult, given the broad spread of versions, so developers should ensure that they know what versions they are implicitly supporting, and to check what version users have installed.

In terms of installation method, I think it's very important to ensure that packages are included in package managers. Even if it is easy to install packages via pip or easy_install in some cases, putting packages in package managers ensures that users will more likely stay up-to-date with the most recent versions.

There is more information still contained in the data than I covered here (for example, some of the above points can be correlated - do the people who do not know how they installed Python correlate with the older versions?). For anyone who is interested in looking at the data, I've placed the files and the scripts I used to make the above plots in a GitHub repository here.

If you have any thoughts about the results, or find anything interesting in the raw data, please leave a comment!