How can we do literate programming for reproducibility, in Python?

Note: Yarden Katz (the author of MISO) sent me the e-mail below, and I asked him if I could post it as a guest-post on my blog. He said yes - so here it is! Feedback solicited.

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Hi Titus,

Hope all is well. A recent tweet you had about Ben Bolker's notes for lit. programming in R (via @hylopsar) made me think about the same for Python, with has been bugging me for a while. Wanted to see if you have any thoughts on getting the equivalent in Python.

What I've always wanted in Python is a way to simultaneously document and execute code that describes an applied analysis pipeline. Some easy way to declaratively describe and document a step-by-step analysis pipeline: Given X datasets available from some web resource, which depends on packages / tools Y, download the data and run the pipeline and ensure that you get results Z. I'd like a language that allows a description that is easily reproducible on a system that's not your own, and forces you to declaratively state things in such a way that you can't cheat with hardcoded paths or quirky settings/versions of software that apply only to your own system. A kind of "literate" pipeline for applied analysis pipelines that allows you to state your assertions/expectations along the way.

One of the main advantages of R over Python is that they have a packaging system that actually works, where as pip/setuptools/distribute are all broken and hard to use, even for Python experts, let alone people who don't want to delve into the guts of Python. So ideally I'd like a system that takes this description of the code and the inputs and executes on a new virtual environment. readthedocs.org does this for documentation, and it's a great way to ensure that you don't have unnoticed hardcoded paths, or Python libraries or packages that cannot be fetched by package managers. Because Python libraries are so hopelessly complicated and broken, and because in comp. bio we rely so often on external tools (tophat version/bowtie version/etc.) this is all the more important. Something that ensures that if you follow these steps, with these data, it'll be automatically installable on your system, and give you the expected output -- no matter what! Knowing that it runs on a server other than your own is key.

Some related tools/ideas that haven't worked very well for me for this purpose, or that only partially address this:

  • IPython notebook: I've had issues with IPython in general, but even when it works, it doesn't address the problem of describing systematically the input and output of the problem, which is key in analysis pipelines. It also doesn't give you a way to state dependencies. If I have a series of calls to numpy/scipy/matplotlib and I want to share that with you, it's good, but an applied analysis pipeline is far more complex than using a bunch of commonly available Python packages to get an output.
  • Unit tests: Standard unit tests are OK for generic software tools. But they don't really make sense for applied analysis pipelines, where the software that you're writing is basically a bunch of analysis (and possibly plotting) code, and not a generic algorithm. You're not testing internal Python library calls, and testing is only a small component of the goal (the other part is describing dependencies and data, and how the pipeline works). You're trying to describe a flow of sequential steps, with forced assertions and conditions for reproducibility. Some of these steps might not be fully automated, or might take far too long to run as a unit test. So what I'm looking for is closer to some kind of sphinx/pydoc document interspersed with executable code, than a plain Python file with unit tests.
  • Ruffus: It's too complicated for most things in my view and it doesn't give you a way to describe the data inputs, etc. It's best for pipelines that consist of internal Python functions that exist within a module, but it gives you no features for describing interaction with external world (external input data, external tools of a specific version whose output you process. One of the few tools that forces you to get things somewhat right is Sphinx/Pydoc. It was for Pycogent which I occasionally contribute it to, and they had configured it so that all the inline examples in the sphinx .rst file were run in real time. That's nice though it's still running only on your own environment and has no features for describing complex data sets / inputs, it was really made for testing library calls within a Python package (like an IPython notebook) -- again, not meant for data-driven pipelines.

The ideal system would even allow you to register analysis pipelines or Python functions in some kind of web system, where each analysis can get a URI and be run with a single click dispatched to some kind of amazon node. But that's not necessary and I don't use the cloud for now.

Would love to hear your thoughts (feel free to share with others who might have views on this.) I've thought about this for a while and never found a satisfactory solution.

Thanks very much!

Best,

--Yarden

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