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This is the version of the project that will be published in Computing in
Science and Engineering (CiSE), Volume 23, Issue 3, Pages 82--91.
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This commit makes several copyediting changes to the appendices and to the
supplement.tex introduction to the appendices.
The ArXiv unofficially increased upload limit of 50 Mb comes from a tweet:
https://nitter.fdn.fr/arxiv/status/1286381643893268483 (archive:
https://archive.today/PdxhT) but not listed on official ArXiv pages. So it
seems safer not to quote a value. The very old value was 0.5 Mb - out of
respect to people with low bandwidth, especially scientists in poor
countries. Tweets are generally not acceptable as "reliable sources" in
en.Wikipedia.
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Until now the appendix only touched upon the archival aspects of scholarly
research producs (data, code, narrative). To help in clarity, the context
of this section has been improved, giving more explanations and examples.
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A few days, CiSE gave us a proof of the edited text and formatted
PDF. After comparing the edited text with our text, I noticed some minor
editorial issues that have been corrected in this commit. The parts that
were wrong (or could be improved in the proof) have been listed and will be
submitted to the journal.
In particular, following the recommendation from the editor, the
biographies were extended with a full listing of each author's affiliation,
I also added our ORCID IDs in the biographies.
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The most basic way to resolve a Software Heritage identifier (SWHID) is to
prefix it with 'https://archive.softwareheritage.org'. However, Roberto Di
Cosmo informed me that SWHIDs are also resolved by 'n2t.net' and
'identifiers.org'.
With this commit, on the first occurance of an SWHID, I added some
explanation of how to resolve it by adding 'http://n2t.org' (since it was
the shorter option).
Some further minor edits were made:
- In the manuscript submission information, instead of "published on
IEEE", I wrote "first published online". The journal name is available
on the top of every page and doesn't include "IEEE", so this hopefully
avoids some confusion for people who don't know CiSE is published by
IEEE.
- The URL with the link to Ubuntu images was moved to footnotes to help
the readablity and better type-setting of the paragraph. A minor edit
was then made in that paragraph to shrink the paragraph by two words
that had occupied a whole line in its end.
- The first comment line in the second listing (Git commands to start a
new branch from Maneage) was slightly edited to avoid the term 'main'
(which could be confused with the branch name after 'git checkout -b
main').
- In the acknowledgements, the paragraph on Maneage commit/branch
information was moved at the top so the people and institutions are
acknowledged immediately after each other.
- Some minor edits were made in the Spanish acknowledgements to fit with
new project names.
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Until now, the SWHIDs were not accessible in the print version of the
paper, they were only hidden as hyper-links within the PDF for readers to
click on. This is not a robust way to use the fruits of Software Heritage
and was kindly highlighted by Roberto Di Cosmo (principle investigator of
Software Heritage) after a first look at the paper.
With this commit, following the recommendation of Roberto, all the URLs are
corrected to print the raw SWHID as a footnote (for example
'swh:1:dir:...', for directories, or 'swh:1:cnt:...', for
contents/files). The click-able link of the SWHID also contains the context
(for example "origin" and etc).
In the process I noticed that the paper submission/acceptance info was not
filled and was also a footnote (which would not be seen if not cited). So
this information (received, accepted and published on IEEE) is now taken
just under the author list on the first page heading.
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The DOI of the paper has been minted by IEEE, so as a step to finalize this
paper, it has been added to the REAMEME.md and the header of all PDF
pages. Along with the DOI in the header, the arXiv and Zenodo links are
also added to the header (they are small, and won't bother the reading).
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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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Having added/modified text in the supplements, Boud is now a copyright
holder of this file too.
I also added 2021 to the copyright years of paper.tex and supplement.tex.
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This commit does some minor copyediting, especially of the
introduction to the supplement. There's no point complaining to
the reader about the word limit of the journal: s/he is not
interested in that. This is not the right place for discussing
journal policy. The need for summarising content and focussing on
key elements of a cohesive argument is fundamental in a world of
information overload. A&A/MNRAS/ApJ/PRD letters are generally
much worse than normal articles in terms of reproducibility
because they have to omit so many details that the reader has
to read the full articles to really know what is done. But the
reality is that letters get read a lot, because they're short
and snappy.
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In the abstract the repeated benefits of Maneage (which are also mentioned
in the criteria) were removed to fit into CiSE's online submission
guidelines. In Section II (Longevity of existing tools), the paragraph that
itemized the following paragrahs as a numbered list has been removed with
the sentence that repeatedly states the importance of reproducibility in
the sciences and some branches of the industry.
With these changes our approximate automatic count has 6277 words. This is
still very slightly larger than the 6250 word limit of the
journal. However, this count is a definite over-estimation (including many
things like page titles and page numberings from the raw PDF to text
conversion). So the actual count for the journal publication should be less
than this.
A few other tiny corrections were made:
- The year of the paper and copyright in 'README.md' was set to 2021. The
copyright of the rest of the files will be set to 2021 after the next
merge with Maneage soon (the years of core infrastructure copyrights has
already been corrected there).
- Mohammadreza's name was added in 'README.md'.
- The line to import the "necessity" appendix has been commented in the
version to have the full paper in one PDF (to be upladed to arXiv or
Zenodo).
- The supplement PDF now starts with '\appendices' so the sections have
the same labels as the single-PDF version.
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Until now the supplement had no introduction for a random reader to see the
purpose of this "Web extra" supplement.
With this commit, an abstract has been added.
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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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