A few weeks ago I wrote about why you should cite open source tools. Although I think citations important, though, there are major problems in relying on them alone to support open source work.
The biggest problem is that papers describing a software library can only give credit to the contributors at the time that the paper was written. The preferred citation for the SciPy library is “Eric Jones, Travis Oliphant, Pearu Peterson, et al”, 2001. The “et al” is not an abbreviation here, but a fixed shorthand for all other contributors. Needless to say many, many people have contributed to the SciPy library since 2001 (GitHub counts 716 contributors as of this writing), and they are unable to get credit within the academic system for those contributions. (As an aside, Google counts about 1,200 citations to SciPy, which is a breathtaking undercounting of its value and influence, and reinforces my earlier point: cite open source software! Definitely don't use this post as an excuse not to cite it!!!)
Not surprisingly, we have had massive contributions to scikit-image since our 2014 paper, and those contributors miss out on the citations to our paper.