Dear Tom, > I suppose this depends on what is meant by "reproducible." > > My goal is to produce a compendium as defined by Gentleman and Lang > (see Gentleman R, Lang DT (2004). "Statistical Analyses and Reproducible > Research." Technical report, Bioconductor Project. URL > http://www.bepress.com/bioconductor/paper2). > > I keep the init.el file as a babel source block with the reproducible > document, so it can be tangled. I also have an editing setup in a babel > source block that activates many of the same features handled by the > init.el file, but also configures the new exporter to look for init.el > (which might have a different name). The filters are all part of the Org > document, too, and get pulled into the init.el file with noweb > references.
My issue here is that this approach might lead to copy-paste "preambles" which may or may not be desirable. I can certainly see the attraction in being able to just tangle the setup. In fact for my thesis I also had a preamble.tex blog in my file. Your proposed setup here is perhaps better in that it uses emacs-lisp. Still, say I'm working on two files A and B. If I fix a bug in "preamble" A I would have to manually copy it over to B. Thus, the main question is how to distribute updates? I guess one could keep a separate file, but then we are back at square one in a way. . . One possibility might be a file structure like this setup.org A/project-A.org A/setup-A.org B/project-B.org B/setup-B.org where A and B both has a block like #+BEGIN_SRC org * Preamlbe :noexport: #+INCLUDE: "../setup.org" #+INCLUDE: "setup-A.org" #+END_SRC To ship it off one would only have to write a command to replacing #+INCLUDE with its content. The exporter could likely be used for this and one could produce an archive version when signing off a project. Even more robust, #+INCLUDE: would look for files in org-directory (it might already do, I didn't check). Am I missing something obvious (probably?) in the above stream of random thoughts? It's kind of a LaTeX-ish way of dealing with it, I guess. > I am able to distribute the compendium, typically as a single > document (sometimes with associated data files produced by an > on-line service that can't be used programmatically), which I > believe is a good step toward reproducibility. Agreed. –Rasmus -- Send from my Emacs