Reproducible research based on open-access papers

Publishing a paper on reproducible research without making it easy for
readers to read the references would defeat the point. Of course we have to
make some compromises with some journals' reluctance to shift towards the
free world, but to satisfy scientific ethics, we should at least provide
clickable URLs to the references, preferably to the ArXiv version if
available [1], and also to the DOI, again, preferably to an open-access
version of the URL if available.

I was not able to fully get this done in the .bst file, so there's an
sed/tr hack done to the .bbl file in `reproduce/analysis/make/paper.mk` to
tidy up commas and spaces.

This commit also reverts some of the hacks in the Akhlaghi IAU Symposium
`tex/src/references.tex` entry, to match the improved .bst file,
`tex/src/IEEEtran_openaccess.bst`, provided here with a different name to
the original, in order to satisfy the LaTeX licence.

[1] https://cosmo.torun.pl/blog/arXiv_refs

1 files changed, 17 insertions, 0 deletions

diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index a216370..08fd766 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -99,12 +99,29 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 	    ln -s $$p/tex/src/references.tex $(texbdir)/references.bib
 	  fi
 
+          # Copy the improved IEEE bst file into the build directory.
+          # The improved bst file provides ArXiv clickable URLs and
+          # if available, open-access URLs based on the DOIs, with
+          # closed-access URLs as a fallback, via https://oadoi.org .
+	  cp -pv $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)
+
           # We'll run LaTeX first to generate the `.bcf' file (necessary
           # for `biber') and then run `biber' to generate the `.bbl' file.
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir);
 	  latex -shell-escape -halt-on-error $$p/paper.tex
 	  bibtex paper
+          # Hack: tidy up eprint+doi style that didn't work in .bst file.
+          # TODO (better): read Part 4 of
+          # http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
+          # and fix the .bst style properly.
+	  cp paper.bbl paper-tmp.bbl \
+	    && sed -e "s/\'/EOLINE/g" paper-tmp.bbl \
+	    | tr -d '\n' \
+	    | sed -e 's/\([0-9]\)\( \|EOLINE\)}/\1}/g' \
+	    | sed -e 's/\([^,]\) *\( \|EOLINE\) *\\eprint/\1, \\eprint/g' \
+	    | sed -e 's/\([^,]\) *\( \|EOLINE\) *\\doi/\1, \\doi/g' \
+	    | sed -e 's/EOLINE/\n/g' > paper.bbl
 	  latex -shell-escape -halt-on-error $$p/paper.tex
 	fi