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Since the addition of the appendix bibliography we hadn't checked the 'make
dist' command, as a result the PDF couldn't be built. With this commit, in
the 'dist' rule, we are now also copying 'appendix.bbl' and the created
tarball could build the PDF properly. Also the 'peer-review' directory is
now also included in the tarball created by './project make dist'.
I also found a small typo in the description of Occam (an 'a' was missing)
and fixed it.
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In preparation for the submission of the revised manuscript, I went through
the full paper and appendices one last time. The second appendix (reviewing
existing reproducible solutions) in particular needed some attention
because some of the tools weren't properly compared with the criteria.
In the paper, I was also able to remove about 30 words, and bring our own
count (which is an over-estimation already) to below 6250.
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After his previous two commits, we discussed some of the points and I am
making these edits following those. In particular the last statement about
Madagascar "could have been more useful..." was changed to simply mention
that mixing workflow with analysis is against the modularity principle. We
should not judge its usefulness to the community (which is beyond our scope
and would need an official survey).
A few other minor edits were done here and there to clarify some of the
points.
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With this commit, I have corrected some minor typos of this appendix.
In addition to that, I also put empty lines to separate subsections and
subsubsections appropiately.
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I ran a simple Emacs spell check over the main body and the two
appendices. All discovered typos have been fixed.
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Until now, in the appendices we were simply using '\ref' to refer to
different parts of the published paper. However, when built in
'--supplement' mode, the main body of the paper is a separate PDF and
having links to a separate PDF is not impossible, but far too complicated.
However, having the links adds to the richness of the text and helps point
readers to specific parts of the paper.
With this commit, there is a LaTeX conditional anywhere in the appendices
that we want to refer the reader to sections/figures in the main body. When
building a separate PDF, the resepective section/figure is cited in a
descriptive mode (like "Seciton discussing longevity of tools"). However,
when the appendices go into the same PDF as the main body, the '\ref's
remain.
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Until now, the build strategy of the paper was to have a single output PDF
that either contains (1) the full paper with appendices in the same paper
(2) only the main body of the paper with no appencies.
But the editor in chief of CiSE recently recommended publishing the
appendices as supplements that is a separate PDF (on its webpage). So with
this commit, the project can make either (1) a single PDF (containing both
the main body and the appendices) that will be published on arXiv and will
be the default output (this is the same as before). (2) two PDFs: one that
is only the main body of the paper and another that is only the appendices.
Since the appendices will be printed as a PDF in any case now, the old
'--no-appendix' option has been replaced by '--supplement'. Also, the
internal shell/TeX variable 'noappendix' has been renamed to
'separatesupplement'.
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As recommended by Lorena Barba (editor in chief of CiSE), we should prepare
the appendices as a separate "Supplement" for the journal. But we also want
them to be appendices within the paper when built for arXiv.
As a first step, with this commit, each appendix has been put in a separate
'tex/src/appendix-*.tex' file and '\input' into the paper. We will then be
able to conditionally include them in the PDF or not.
Also, as recommended by Lorena, the general "necessity for reproducible
research" appendix isn't included (possibly going into the webpage later).
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