Archive for November 2013

Python as a platform for reproducible research

November 19, 2013

The other day I was looking at the release notes for the recently published release 1.8 of NumPy, the library that is the basis for most of the Scientific Python ecosystem. As usual, it contains a list of new features and improvements, but also sections such as “dropped support” (for Python 2.4 and 2.5) and “future changes”, to be understood as “incompatible changes that you should start to prepare for”. Dropping support for old Python releases is understandable: maintaining compatibility and testing it is work that needs to be done by someone, and manpower is notoriously scarce for projects such as NumPy. Many of the announced changes are in the same category: they permit removing old code and thus reduce maintenance effort. Other announced changes have the goal of improving the API, and I suppose they were more controversial than the others, as it is rarely obvious that one API is better than another one.

From the point of view of reproducible research, all these changes are bad news. They mean that libraries and scripts that work today will fail to work with future NumPy releases, in ways that their users, who are usually not the authors, cannot easily understand or fix. Actively maintained libraries will of course be adapted to changes in NumPy, but much, perhaps most, scientific software is not actively maintained. A PhD student doing computational reasearch might well publish his/her software along with the thesis, but then switch subjects, or leave research altogether, and never look at the old code again. There are also specialized libraries developed by small teams who don’t have the resources to do as much maintenance as they would like.

Of course NumPy is not the only source of instability in the Python platform. The most visible change in the Python ecosystem is the evolution of Python itself, whose 3.x series is not compatible with the initial Python language. It is difficult to say at this time for how long Python 2.x will be maintained, but it is well possible that much of today’s scientific software written in Python will become difficult to run ten years from now.

The problem of scientific publications becoming more and more difficult to use is not specific to computational science. A theoretical physicist trying to read Isaac Newton’s works would have a hard time, because the mathematical language of physics has changed considerably over time. Similarly, an experimentalist trying to reproduce Galileo Galilei’s experiments would find it hard to follow his descriptions. Neither is a problem in practice, because the insights obtained by Newton and Galilei have been reformulated many times since then and are available in today’s language in the form of textbooks. Reading the original works is required only for studying the history of science. However, it typically takes a few decades before specific results are universally recognized as important and enter the perpetually maintained canon of science.

The crucial difference with computations is that computing platforms evolve much faster than scientific research. Researchers in fields such as physics and chemistry routinely consult original research works that are up to thirty years old. But scientific software from thirty years ago is almost certainly unusable today without changes. The state of today’s software thirty years from now is likely to be worse, since software complexity has increased significantly. Thirty years ago, the only dependencies a scientific program would have is a compiler and perhaps one of a few widely known numerical libraries. Today, even a simple ten-line Python script has lots of dependencies, most of the indirectly through the Python interpreter.

One popular attitude is to say: Just run old Python packages with old versions of Python, NumPy, etc. This is an option as long as the versions you need are recent enough that they can still be built and installed on a modern computer system. And even then, the practical difficulties of working with parallel installation of multiple versions of several packages are considerable, in spite of tools designed to help with this task (have a look at EasyBuild, hashdist, conda, and Nix or its offshoot Guix).

An additional difficulty is that the installation instructions for a library or script at best mention a minimum version number for dependencies, but not the last version with which they were tested. There is a tacit assumption in the computing world that later versions of a package are compatible with earlier ones, although this is not true in practice, as the example of NumPy shows. The Python platform would be a nicer place if any backwards-incompatible change were accompanied by a change in package name. Dependencies would then be evident, and the different incompatible versions could easily be installed in parallel. Unfortunately this approach is rarely taken, a laudable exception being Pyro, whose latest incarnation is called Pyro4 to distinguish it from its not fully compatible predecessors.

I have been thinking a lot about this issue recently, because it directly impacts my ActivePapers project. ActivePapers solves the dependency versioning problem for all code that lives within the ActivePaper universe, by abandoning the notion of a single collection of “installed packages” and replacing it by explicit references to a specific published version. However, the problem persists for packages that cannot be moved inside the ActivePaper universe, typically because of extension modules written in a compiled language. The most fundamental dependencies of this kind are NumPy and h5py, which are guaranteed to be available in an ActivePapers installation. ActivePapers does record the version numbers of NumPy and h5py (and also HDF5) that were used for each individual computation, but it has currently no way to reproduce that exact environment at a later time. If anyone has a good idea for solving this problem, in a way that the average scientist can handle without becoming a professional systems administrator, please leave a comment!

As I have pointed out in an earlier post, long-term reproducibility in computational science will become possible only if the community adopts a stable code representation, which needs to be situated somewhere in between processor instruction sets and programming languages, since both ends of this spectrum are moving targets. In the meantime, we will have to live with workarounds.