I want to publish the software package I've written for my graduate work along with a paper describing the package. So far I've been considering liberal licenses such as BSD.
However, I am now aware that publishing your code may involve an agreement to the journal's licensing terms (cmp. e.g. this question) or even transfer of copyright. All this is undesirable. Are there any obvious choices concerning the journal? My field is physics. Do you have experience founding a BSD-license style open source project and publishing an accompanying paper?