Yes, if you publish, you're required to release everything necessary for a practitioner reasonably skilled in the art to reproduce your results, without undue effort. For example, releasing a tarball of source code missing the Makefile that runs the arcane build process is not within the spirit of free software and you will be soundly ridiculed and if GPL is involved may be sued. Dumping a database that, together with your paper, still requires n > 1 grad-student-years of effort to reproduce is not really open science, although it's a huge step up from Elsevier. Is this broadly understood? Probably not, but it is at least well known by some. Honestly, free software people have been working out these "reproducibility" issues in practice for decades before the biologists even got on the bus.
If you publish your software, you are required to release everything needed to develop it further, yes.
However, if you publish your paper, you are not required, under the free software principles.
If I am wrong, show me where the FSF/GNU say that.
I believe your argument is that there's a clear parallel to publishing a paper and publishing the software.
However, there's also a clear parallel to, say, publishing an internet service based on free software, and publishing the software. This lead to the AGPL.
The GPL does not have that requirement, which means it isn't a free software principle. It could have - I think I've heard Eben Moglen say it was discussed early on. But if so, then having a telnet server, or ftp server, or anything reacting to the network, would require the ability to download the source.
> free software people have been working out these "reproducibility" issues in practice for decades before the biologists even got on the bus.
While biologists were working out other "reproducibility" issues long before there were buses.
You're correct about FSF/GNU having narrow focus. Also that the GPL doesn't say anything about what biologists can't publish. Analogically we can make the arguments but we can't attribute these arguments to the FSF. Whether the west coast hackers influenced the open access science movements -- it's obvious that they did, this is not all post hoc parallels that everyone missed at the time.
My argument is that that analogy doesn't follow from free software principles.
If it did, then it would follow that if you publish the paper, you're obligated to release your source.
And we don't see that coming out of the free software movement. We do see that coming out of the open data/open science movement.