Robin's Blog

My 2015 Python life

My last post about my favourite ‘new’ (well, new to me) Python packages seemed to be very well received. I’ll post a ‘debrief’ post within the next few weeks, reflecting on the various comments that were made on Hacker News, Reddit and so on, but before that I want to post a slightly more personal post about my work with Python during the last year. It’s been quite a big year for me in terms of my Python work – so lets get started!

My packages

At the beginning of 2015 I had four modules published on PyPI; now I have seven! Lets have a look at each of them in turn:

Py6S

Py6S is my Python interface to the 6S Radiative Transfer Model (a model used to simulate how light passes through the atmosphere). It is a fairly specialist tool so will never get record numbers of downloads, but I’ve been impressed with number of users it has gained over the last year. It’s taken a while, but it seems to have started being used routinely by a range of scientists at various organisations including NASA!

The major change to Py6S in 2015 has been adding support for Python 3. This was actually meant to have been done in July 2014, but I think managed to make some sort of awful mistake with Git and revert the wrong commit… Anyway, it’s all working for Python 2 and Python 3 now! Most of the rest of the changes have just been small bugfixes, adding tests and so on.

Downloads in last month: ~1700

daterangeparser

daterangeparser is a module to parse, you guessed it…date ranges. For example, it will take something like ’20th – 29th July 2014′ and create two datetime objects to represent the start and end dates. I first released it in April 2012 and it reached 1.0 in October 2013. I haven’t used it much recently, but other people seem to have found it and started using it – and submitting bug reports and pull requests! This really shows one of the huge benefits of open-source code: I’ve done very little with the code, but I’ve had nine pull requests adding new functionality and fixing bugs, which is great! I’m really glad that others can benefit from it.

Downloads in last month: ~1700

recipy

recipy is a new module for reproducible research in Python which was first released in August 2015. I’ve explained the story behind recipy elsewhere, but in brief: I created the first version at the Collaborations Workshop 2015 Hack Day (which my team won!), and we worked to improve it, before presenting at EuroSciPy 2015. The best way to find out how it works is to watch the video of my talk at EuroSciPy 2015.

Anyway, recipy was the first time that anything I had created went ‘viral’ (well, in a relatively minor way!). There were a lot of tweets about it, and a good discussion on reddit, and this led to a lot of downloads, quite a few contributions, and even a Linux Journal article! Overall there have been over 200 commits, 7 merged PRs, 52 closed issues and 7 released versions – not bad for a module released only six months ago!

Downloads in the last month: ~8800

vanHOzone

I’ve already written a post about my implementation of the van Heuklon Ozone model – and this year I turned it into a proper package and released it on PyPI. Basically, I just got fed up with having to install it from git on new machines, as a lot of my scientific code requires it! It’s not particularly impressive – but it is useful to get a simple (computationally efficient) estimation of atmospheric ozone concentrations.

The only real change that I did this year was to make a conda package for it – see my previous post for details.

Downloads in the last month: ~110

Others

Two other modules of mine have been ticking along with no work done to them: PyProSAIL (an interface to the ProSAIL model of canopy reflectance) and bib2coins (a tool to convert from BibTeX to COINS metadata for inclusion on webpages). Whenever I’ve used them they’ve worked fine for me – and I assume that either no-one else is using them, or that everything is working fine for them too (probably the former!).

Downloads in the last month: ~260 and ~100 respectively

Conferences

For the first time this year I attended a conference designed entirely for programmers (all the conferences I’ve attended before have been for academics)…and it was great! I really enjoyed myself at EuroSciPy 2015: lots of the talks were interesting, my talk seemed to go down well (I won one of the Best Talk awards!), I managed to contribute usefully during the sprints, I met loads of interesting people…and even took my wife with me and introduced her to the Python programming community (you can see us both in the photo below). She was very proud to contribute a couple of PRs to the scikit-image project.

My wife and I at the EuroSciPy skimage sprint (photo by Juan Nunez-Iglesias)

Things I’ve (finally) started using…

This year I have finally started doing various things that I should have been doing for many years. A non-exhaustive list includes:

• I’m now using Python 3 by default (hooray!). I can blame one of my colleagues in the Flowminder team for this – he insisted that we should write our code for mobile phone data analysis in Python 3 (not even trying to support Python 2) and I agreed, and now haven’t looked back! I’m now trying to ensure that as much of my code as possible (and definitely all of my code released to PyPI) supports Python 3…and I always start with Python 3 by default. The only code that I haven’t yet moved to Python 3 is the main algorithm I developed during my PhD…not because it can’t be converted, but just because I’ve got more important things to do to the code at the moment, and as I’m the only person using it (at the moment…) it isn’t a major problem.
• I’m writing code that conforms to PEP8…at long last! I was doing quite a lot of the ‘really stupidly obvious’ bits of PEP8 anyway, but I’m now trying to stick very closely to PEP8, and it has made a noticeable difference in terms of the readability of my code. I have chosen to ignore a few bits of PEP8 (such as the 80 character line length, which I find is too short by the time you’ve had a couple of levels of indentation), but overall I like it. I use the flake8 tool to check this, and the linter and linter-flake8 packages for Atom to automatically check it while I’m coding. I must admit that most of this is my wife’s ‘fault’, as she was introduced to PEP8 as a non-negotiable requirement for submitting PRs to skimage while she was at EuroSciPy, and never considered that there was another way to write Python code (I sometimes wondered if she thought Python would raise a NotPEP8Compliant exception if she didn’t use PEP8!), and so – like a lot of good things – I picked it up from her.
• I’ve written a lot of Python code this year, and for the first time a lot of this code has been written in a team – so I’ve learnt a lot about how to write maintainable, understandable code – and what problems will come back and bite me later and should really be sorted at the beginning.
• I’ve started blogging a lot more, and some of my blog posts have actually become quite popular (particularly my post about my favourite 5 ‘new’ Python packages). I’ve also started a series called Previously Unpublicised Code, in which I talk about various pieces of code that I’ve put on Github over the years but have never really publicised or talked about at all. This has forced me to tidy up a lot of my code on Github – and I’ve made it a rule that I won’t post about any code unless it has a README, a LICENSE, and is mostly PEP8-compliant.

So, that’s mostly what I’ve been up-to in 2015 from a Python perspective – what have you been doing in Python in 2015?

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This post originally appeared on Robin's Blog.

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Categorised as: Programming, Python