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2021-06-11Published version in CiSEMohammad Akhlaghi-1/+1
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.
2021-06-08Several minor edits, removed exact value of arXiv's size-limitBoud Roukema-1/+1
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.
2021-06-08Improved appendix on archivalMohammad Akhlaghi-1/+1
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.
2021-05-12Implemented changes of first proof by CiSEMohammad Akhlaghi-2/+2
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.
2021-04-29Software Heritage resolver info in first footnoteMohammad Akhlaghi-1/+1
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.
2021-04-28Software Heritage IDs (SWHIDs) now printed in PDFMohammad Akhlaghi-3/+3
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.
2021-04-25DOI added to README and paper's headerMohammad Akhlaghi-1/+1
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).
2021-01-05Polished main paper and appendices after a full re-readMohammad Akhlaghi-2/+2
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.
2021-01-03Added Boud as copyright holder of supplement.texMohammad Akhlaghi-1/+2
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.
2021-01-03Minor copyeditingBoud Roukema-8/+8
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.
2021-01-03Cleaned abstract and Section II to fit word limitMohammad Akhlaghi-0/+1
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.
2021-01-03Added abstract for supplementMohammad Akhlaghi-1/+13
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.
2021-01-02Supplement (containing appendices) optionally built separatelyMohammad Akhlaghi-0/+85
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'.