Question: An ESR essay about software design, and how it applies to Bioconductor
15.6 years ago by
Alex F. Bokov • 50
Alex F. Bokov • 50 wrote:
So here goes, I am about to risk getting myself blacklisted by the very people I can least afford to be blacklisted by, and at the very start of my career no less. Why am I taking this risk? Because I love Bioconductor, it's the most useful thing currently installed on my PC, and I'm deeply grateful to the developer and user community for making such a wonderful tool. The following constructive criticism is how I hope to make it better. Here is an essay by Eric S. Raymond describing the difficulties he had configuring a software package on Linux. Obviously the last person you'd think of as "computer illiterate", "lazy", or "clueless". http://www.catb.org/~esr/writings/cups-horror.html Once you wade through the technical minutia of his specific software struggle, the main message appears to be that software is often written by individuals who are so knowledgeable in their particular field that their idea of "obvious", "self explanatory", "intuitive", "user friendly", and even "adequately documented" may be completely different from the rest of humanity! I immediately thought of certain BioC packages I've recently bashed my head over (and over and over). At the end of the essay ESR presents a checklist for telling whether your software suffers from problems similar to the ones he describes. For the benefit of any package developers/maintainers who may still be reading this, here's my version of that checklist as revised specifically for Bioconductor: 1. What does the package look like to a computer person who isn't a statistician or a statistician who isn't a computer person? What would be the most obvious thing someone unfamiliar with your package would try to use it for... and if they did, would they succeed after having done nothing more than read the manpage? 2. Is there any dialogue in the Tcl widgets which is a dead end, without giving guidance on what the choices actually do? (although if you read ESR's essay you might conclude that there's no point to even having widgets, since a GUI does not automatically translate into user friendliness) 3. The requirement that end-users read documentation is NOT a sign of failure for a program such as R which mostly lacks a UI... but... * Is every argument, method, and slot of every non-private object documented in the manpage *for that object* (rather than referring to some other manpage which in turn refers to another manpage, ad nauseum)? * Are the usage examples you give in the manpage simple, general, and comprehensible both to statisticians who aren't computer people and computer people who aren't statisticians? Hint: gratuitous use of functions that aren't from the package you're documenting reduces comprehensibility. * Does the documentation rely on references to hardcopy publications to explain crucial portions of the object's functionality instead of using external references as supplementary/background material? * If there is a significant number of usage scenarios where the default argument values will be inappropriate, is the user warned? * Are the manpages in sync with the current package version? 4. Do you ever find yourself using any phrase resembling "The syntax is just like it is for the S-Plus version"? 5. Does your project welcome and respond to usability feedback from non-expert users? 6. Do error messages give enough information to be able to distinguish between malformed input/arguments, platform limitations (memory, drive space, access permissions), problems in R itself, and other ("other" presumably being the real bugs)? Thank you for your patience in reading this. I don't pretend to understand the technical complexity of your work, nor your motivations for doing it. However, if you do write open source software such as Bioconductor packages, it would be logical to at least assume that you want other people to use your software. Hopefully the above considerations will assist in making that happen.
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