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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).
2021-04-09Implemented EiC (Lorena Barba) comments, and added final reviewMohammad Akhlaghi-49/+47
The email notice of the final acceptance of this paper in CiSE has been included in the project and the stylistic points that were raised by the editor in chief (EiC) have also been implemented. The most important points were: - Including citations within the text structure (as if they would be footnotes), so things like "see \cite{...}" should have been changed. - Hyperlinks should be printed as footnotes (because the journal gets actually printed). Also, to avoid the second listing breaking between pages, it has been moved to after the next paragraph.
2021-04-09Minor corrections on previous copyeditMohammad Akhlaghi-1/+1
Being immutable doesn't necessary mean that something is always present, so an "always present" was also added for the reason we recommend a Git hash. The end of the sentence was also slightly summarized to allow the extra few words. The re-wording of the conclusion of Active papers, was great! I just changed the "likely" to "possible", because as Konrad mentioned in Commit a63900bc5a8, he is now using Guix.
2021-04-09Minor copyeditsBoud Roukema-2/+2
These are minor last minute copyedits for recently added text, e.g. a git hash is not literally a timestamp.
2021-04-09Corrected Roberto's affiliation and emailMohammad Akhlaghi-3/+4
Roberto has recently moved to a new position as professor in the Universidad Internacional de La Rioja. With this commit, his short bio and email address have thus been updated in the main paper to reflect this.
2021-04-09Changed all gitlab.com URLs to git.maneage.orgMohammad Akhlaghi-4/+4
Until now, we were primarily linking people to the Gitlab fork of this paper. However, since this paper is part of Maneage, its main repository is on Maneage's own server at http://git.maneage.org/paper-concept.git With this commit therefore, all the gitlab.com URLs have been corrected to owr own Git server. While looking into Git-related points, I also noticed that in the demo code listing showing how to clone Maneage and start a new project, we were using Git's old/depreciated 'master' name. Git (and almost all common repositories) now use 'main' as the default branch name, so this has also been corrected here.
2021-04-09Acknowledged Peter WittenburgMohammad Akhlaghi-1/+2
I attended one of Peter Wittenburg's talks in the context of RDA on the Canonical Workflow Frameworks for Research (CWFR). Afterwards I got in touch with him about Maneage and this paper. He kindly read the paper was very supportive of it with positive/encouraging feedback. It was thanks to that discussion that I added CWFR in the discussion (in the previous commit). But since that commit was focused on IAA's suggestions, I am acknowledging Peter here.
2021-04-09Comments by IAA's AMIGA team implementedMohammad Akhlaghi-8/+19
The AMIGA team at the Instituto Astrofísica Andalucía (IAA) are very active proponents of reproducibility. They had already provided very constructive comments after my visit there and many subsequent interactions. So until now, the whole team's contributions were acknowledged. Since the last submission, several of the team members were able to kindly invest the time in reading the paper and providing very useful comments which are now being implemented. As a result, I was able to specifically thank them in the paper's acknowledgments (Thanks a lot AMIGA!). Below, I am listing the points in the order that is shown in 'git log -p -1' for this commit. - Javier Moldón: "PM is not defined. First appearance in the first page". Thanks for noticing this Javier, it has been corrected. - Javier Moldón: "In Section III. PROPOSED CRITERIA FOR LONGEVITY and Appendix B, you mention the FAIR principles as desirable properties of research projects and solutions, respectively which is good, but may bring confusion. Although they are general enough, FAIR principles are specifically for scientific data, not scientific software. Currently, there is an initiative promoted by the Research Data Alliance (RDA), among others, to create FAIR principles adapted to research software, and it is called FAIR4RS (FAIR for Research Software). More information here: https://www.rd-alliance.org/groups/fair-4-research-software-fair4rs-wg. In 2020 there was a kick-off meeting to divide the work in 4 WG. There is some more information in this talk: https://sorse.github.io/programme/workshops/event-016/. I have been following the work of WG1, and they are about the finish the first document describing how to adapt the FAIR principles to software. Even if all this is still work in progress, I think the paper would benefit from mentioning the existence of this effort and noticing the diferences between Data and Software FAIR definitions." Thanks for highlighting this Javier, a footnote has been added for this (hopefully faithfully summarizing it into one sentence due to space limitations). - Sebastian Luna Valero: "Would it be a good idea to define long-term as a period of time; for example, 5 years is a lot in the field of computer science (i.e. in terms of hardware and software aging), but maybe that is not the case in other domains (e.g. Astronomy)." Thanks Sebastian, in section 2, we do give longevity of the various "tools" in rough units of years (this was also a suggestion by a referee). But of course the discussion there is very generic, so going into finer detail would probably be too subjective and bore the reader. - Sebastian Luna Valero: "Why do you use git commit eeff5de instead of git tags or releases for Maneage? Shown for example in the abstract of the paper: "This paper is itself written with Maneage (project commit eeff5de)." Thanks for raising this important point, a sentence has been added to explain why hashes are objective and immutable for a given history, while tags can easily be removed or changed, or not cloned/pushed at all. - Susana Sanchez Exposito: "We think interoperability with other research projects would be important, do you have any plans to make maneage interoperable with, for example, the Common Workflow Language (CWL)?". Thanks a lot for raising this point Susana. Indeed, in the future I really do hope we can invest enough resources on this. In the discussion, I had already touched upon research objects as one method for interoperability, there was also a discussion on such generic standards in Appendix A.D.10. But to further clarify this point (given its importance), I mentioned CWL (and also the even more generic CWFR) in the discussion. - Sebastian Luna Valero: "Regarding Apache Taverna, please see:" https://github.com/apache/incubator-taverna-engine/blob/master/README.md Thanks a lot for this note Sebastian! I didn't know this! I wrote this section (and visited their webpage) before their "vote"! It was a surprize to see that their page had changed. I have modified the explanation of Taverna to mention that it has been "retired" and use the Github link instead. - Sebastian Luna Valero: "Page 21: 'logevity' should be 'longevity'." Thanks a lot for noticing this! It has been corrected :-). - Javier Moldón: "There is a nice diagram in Johannes Köster's article on data processing with snakemake that I find very interesting to show some key aspects of data workflows: see Fig 1 in https://www.authorea.com/users/165354/articles/441233-sustainable-data-analysis-with-snakemake " This is indeed a nice diagram! I tried to cite it, but as of today, this link is not a complete paper (with no abstract and many empty section titles). If it was complete, I would certainly have cited it in Snakemake's discussion. - Javier Moldón: "Regarding the problem mentioned in the introduction about PM not precisely identified all software versions, I would like to mention that with Snakemake, even if the analysis are usually constructed using other package managers such as conda, or containers, you don't need to depend on online servers or poorly-documented software versions, as you can now encapsulate an analysis in a tarball containing all the software needed. You still have long-term dependency problems (as you will need to install snakemake itself, and a particular OS), but at least you can keep the exact software versions for a particular platform." Thanks for highlighting this Javier. This is indeed better than nothing, we have already discussed the dangers of this "black box" approach of archiving binaries in many contexts, and many package managers have it. So while I really appreciate the point (I didn't know this), to avoid lengthening the paper, I think its fine to not mention it in the paper.
2021-01-07Removed all \new highlights after submission of reviewMohammad Akhlaghi-71/+68
With the submission of the revision (which highlighted all the relevant parts to the points the referees raised in the submitted PDF) it is no longer necessary to highlight these parts. If we get another revision request, we can add new '\new' parts for highlighting.
2021-01-05Polished main paper and appendices after a full re-readMohammad Akhlaghi-59/+70
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.
2021-01-03Spell check on main body and appendicesMohammad Akhlaghi-23/+15
I ran a simple Emacs spell check over the main body and the two appendices. All discovered typos have been fixed.
2021-01-03Minor corrections to the existing tools appendixRaul Infante-Sainz-2/+2
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 (5 lines and 1 line, respectively).
2021-01-03Minor corrections to the main body textRaul Infante-Sainz-26/+26
With this commit, I had a look at the paper and correct some minor typos. When possible, I tried to simplify some phrases to have less number of words. To do that, I added some hypens when I considered it could be necessary/possible.
2021-01-03Added Boud as copyright holder of supplement.texMohammad Akhlaghi-6/+6
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-1/+1
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-16/+11
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.
2021-01-02Supplement (containing appendices) optionally built separatelyMohammad Akhlaghi-14/+8
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'.
2021-01-01Minor edits in the acknowledgement and biographiesMohammad Akhlaghi-63/+29
Since we have a long list of Copyright statements at the top, I thought its easier to just move the copyright notice to the top of 'paper.tex' also. In the acknowledgments, the paragraph on Maneage was slighltly summarized to save a few words and still be clear. Also, the long name of the Japanese Ministry of Education, Culture, Sports, Science, and Technology, was summarized to Japanese MEXT. In the biographies, the '-at' (replacing '@' in the emails) was changed to '-AT' to be more clear to the eye that its just a place holder.
2020-12-30Each appendix moved to a separate .tex fileMohammad Akhlaghi-1087/+2
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).
2020-12-29Added Mohammadreza's copyright notice on paper.texMohammad Akhlaghi-0/+1
After adding Mohammadreza as an author of the paper, we forgot to add him as a copyright holder at the start of the paper.
2020-12-29Copyedit on Appendix ABoud Roukema-45/+45
This commit makes many small wording fixes, mainly to Appendix A. It also insert "quotes" around some of the titles fields in 'tex/src/references.tex', since otherwise capitalisation is lost (DNA becomes Dna; 'of Reinhart and Rogoff' becomes 'of reinhart and rogoff'; and so on). I didn't do this for all titles, because some Have All Words Capitalised, which blocks the .bib file from choosing a consistent style.
2020-12-29Mohammadreza Khellat added as an authorMohammadreza Khellat-4/+11
Mohammadreza has made significant contributions to the text of the paper and also the source. However his contributions to the text came after the initial submission, so until now, he was not added as an author. The reason we waited for this was that no responses were given by CiSE editors, on the inquiry of the possibility of adding a new author at this phase. With this commit, following approval from the editors, Mohammadreza's information has been added to the manuscript as an author to refrain from delays in submitting the manuscript revision. While merging with the 'master' branch, Mohammad also done some minor edits to the other biographies to follow a similar format.
2020-12-28Minor edits, updated citation to published Menke+20 paperMohammad Akhlaghi-32/+36
Some minor edits were made to the paper to shorten it. In particular the example of IPOL was removed from the main body of the paper, and we'll just rely on the more extensive review of IPOL in the appendix. I also updated the referee report to account for the new Appendix A that is just an extended introduction. Also, I noticed that the Menke+20 paper that we replicate here has recently been published in the iScience journal. So its bibliography was updated from the bioarXiv information to the journal information. Also, the number of words (after removing abstract and captions and accounting for figures) is now only printed when the project is built with '--no-appendix'. This was done because this information is extra/annoying/unnecessary for the case where there is an appendix.
2020-12-28The old/long introduction is now an appendix on necessityMohammad Akhlaghi-0/+87
In the first/long draft of this work, we had a good introduction on the necessity of reproducibility. But we were forced to remove it because of word-count limits. Having moved a major portion of the previous work into the appendices, I thought it would be good to put that introduction as a first appendix also, focused on the necessity for reproducibile research.
2020-12-27Edits to snapshot size argument, minor edits here and thereMohammad Akhlaghi-22/+25
Following Boud's point in the previous commit, I tried to clarify the point in the text that we are only talking about hand-written source files: in short, in this part of the paper, we are not talking abou the version/snapshot for arXiv which needs figures and many extra automatically built files. We are just talking about the raw, hand-written files. Trying to convince people how good it is to keep the raw files separate from automatically generated files ;-). Also, while looking around in other parts of the main body of the paper, I tried to edit/clarify a few points and summarize/shorten others.
2020-12-27Fix typos; snapshot sizeBoud Roukema-4/+4
This commit fixes 'automaticly', 'mega byte', 'terra byte'. It also changes 'will be far less than a mega byte' to 'should be less than a megabyte'. The reason for 'should' is that in some cases, providing a small data set in the package is useful, as in [1]. Of course, [1] would be only 0.9 Mb in size, including the data sets, instead of 1.3 Mb, if the author, whoever that may happen to be, had excluded the useless (produced) file 'paper-tmp.eps'. :P Case [2] is 0.4 Mb. These two tar archives are for ArXiv, so they also contain produced .eps files. So maybe in principle 'far less than' is right. However, on neither [3] nor [4], trying to follow the recommendations :), are any of the "useful" versions of single file archives smaller than the ArXiv version. The git bundles are bigger because of the git history, and the 'software' archives are 0.5 to 0.6 Gb because they include almost everything. However, stating something that is possible in principle but not done in practice would be misleading. So I would not include 'far less'. [1] https://zenodo.org/record/3951152/files/subpoisson-252cf1c-arXiv.tar.gz [2] https://zenodo.org/record/4062461/files/elaphrocentre-724a7c8-arXiv.tar.gz [3] https://zenodo.org/record/3951152 [4] https://zenodo.org/record/4062461
2020-12-27Fix multiply defined labelsBoud Roukema-5/+5
This commit fixes the labels alliez19, claerbout1992, schwab2000 which were multiply defined. The problem was using \citeappendix instead of \cite for these in the appendix, even though they are first used in the official part of the article. You must do './project make clean' before recreating the pdf in order for this to compile correctly. (Otherwise you'll waste time re-using old files; this means that one of our 'make' dependencies could in principle be improved.) With this change, these references in the pdf are (for me) correct clickable links back to [5], [1], [11], respectively. [If you use xpdf (poppler library), remember the 'b' key for navigate back from a clicked internal link quickly.] This way you can quickly navigate between the appendix text and the references used, and you avoid LaTeX warning about 'multiply defined labels'.
2020-12-27Copyediting, based on the not contractionBoud Roukema-23/+23
This commit provides a little bit of minor copyediting, mainly in the appendices, based on and around changing the casual 'isn't', 'don't' and other contractions with 'not' to a less casual style of language. A few of the changes aim to improve the meaning in tiny ways.
2020-12-27Minor: add missing wordBoud Roukema-1/+1
The sentence sounds better with 'the'.
2020-12-26Added example of recent CentOS terminationMohammad Akhlaghi-6/+7
It was recently announced by both RedHat[1] and CentOS[2] that CentOS 8 (which was meant to end LTS at 2030) will be terminated 8 years early (by the end of 2021). This is a perfect example of the longevity issues when relying on third-party providers. With this commit, I added this as a parenthesis after mentioning Ubuntu's LTS web address. Some minor edits were also done in other parts of this paragraph. [1] https://www.redhat.com/en/blog/centos-stream-building-innovative-future-enterprise-linux [2] https://blog.centos.org/2020/12/future-is-centos-stream
2020-12-07Proprietary obsolescence added in free software criteriaMohammad Akhlaghi-1/+1
Today, Richard Stallman sent a mail in 'info-gnu@gnu.org' (GNU's public announcements mailing list) about proprietary obsolescence (or planned obsolescence) [1]. After looking into it, I saw there is actually a Wikipedia page for this concept. Since it direclty relates to our Free software criteria, I thought its good to use this technical term there. [1] https://www.gnu.org/proprietary/proprietary-obsolescence.html [2] https://en.wikipedia.org/wiki/Planned_obsolescence
2020-12-04Comparison with Jupyter: added that different editors can be usedMohammad Akhlaghi-3/+3
I just remembered that in the paragraph we compare with Jupyter, another important point is that with based on the modularity principle, people can choose their favorite text editor and aren't limited to one. I also tried to remove redundant parts to avoid adding too many extra words.
2020-12-02Minor edits in newly added parts on statistical verificationMohammad Akhlaghi-2/+3
Thanks a lot Boud for adding that script in your own project and linking it here. Since the raw file (without context of the whole project) is very hard to understand for the users, I switched the URL to the navigable URL the link is actually on the filename. It will always show the most recent version of this script, not the particular snapshot of now. But infact that is better, since we can make it better and improve it over time. Maybe even by the end of this paper's referee review will be able to include it in Maneage's core branch. I also removed the link to this discussion at the first paragraph of Section IV (proof of concept). Since that is just the introduction, and going into this level of detail there could be confusing for the readers. Having the name of the script in the proper place is more direct and understandable for the readers. Thanks again Boud for the nice work on this ;-).
2020-12-02URL of statistical verificationBoud Roukema-2/+2
This commit adds the SWH URL of the statistical verification script to the paper and tidies up the corresponding answer in '1-answer.txt'. The script file includes more extensive documentation than the earlier 'make' version of the method.
2020-12-02Modularity in file structure discussed with other minor editsMohammad Akhlaghi-26/+50
While going through Mohammad-reza's recent two commits, I noticed that we had missed an importnat discussion on modularity in this version of the paper (discussing how file management should also be modular resulting in cheaper archival, and thus better longevity), so a few sentences were added under criteria 2 (Modularity). Mohammad-reza's edits were also generally very good and helped clarify many points. I only reset the part that we discuss the problems with POSIX, and not being able to produce bitwise reproducible software (which systems like Guix work very hard at, and thus need root permissions). I felt the edit missed the main point here (that while bitwise reproducibility of the software is good, it is not always necessary).
2020-12-02Modified POSIX related discussionsMohammadreza Khellat-15/+14
Before this commit, there were discussions in different sections related to POSIX compliance and features. Since the relevant Cmpleteness criterion has been changed to execution within a Unix-like OS, such dicussions had to be modifies as well. With this commit, the parts that were related to condition (1) of the Completeness criterion have been modified to be relevant to new Unix-like OS requirement. Also, few spelling problems were fixed.
2020-12-02Minor modification of Completeness criterion conditionsMohammadreza Khellat-6/+6
Before this commit, condition (1) for the Completeness criterion was referring to POSIX compliance. POSIX is a very detailed dynamic standard which goes under revision continuously and not a lot of operating systems, GNU/Linux included are completely/officially POSIX-compliant. Furthermore, not all sections of the huge 4000 pages standard are really important specifically to the current Maneage functionality. With this commit, condition (1) has been replaced by a looser condition of execution within a Unix-like OS. Also since the term environment might have been mistaken with the term "Operating Environment", it was replaced by the unmistakable term "environment variables" in conditions (3) and (5). Last but not least, condition (2) was made more restrict by adding ASCII encoding as the condition for storing the plain text files. TO-DO: POSIX could contain valuable ideas regarding portability of programming practices. These can be taken advantage of later in providing necessary and sufficient conditions for project completeness. Another idea could be to make LFS construct or something else as a sharp definition for what we mean by minimal Unix-like OS.
2020-12-01Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-3/+4
Some minor conflicts that came up during the merge were fixed.
2020-12-01Default paper: macros available for date of commits citedMohammad Akhlaghi-4/+7
Until now, Maneage only provided the commit hashes (of the project and Maneage) as LaTeX macros to use in your paper. However, they are too cryptic and not really human friendly (unless you have access to the Git history on a computer). With this commit, to make things easier for the readers, the date of both commits are also available as LaTeX macros for use in the paper. The date of the Maneage commit is also included in the acknowledgements. Also, the paragraph above the acknowledgements has been updated with better explanation on why adding this acknowledgement in the science papers is good/necessary.
2020-12-01IMPORTANT: organizational improvements in Maneage TeX sourcesMohammad Akhlaghi-170/+96
This only concerns the TeX sources in the default branch. In case you don't use them, there should only be a clean conflict in 'paper.tex' (that is obvious and easy to fix). Conflicts may only happen in some of the 'tex/src/preamble-*.tex' files if you have actually changed them for your project. But generally any conflict that does arise by this commit with your project branch should be very clear and easy to fix and test. In short, from now on things will even be easier: any LaTeX configuration that you want to do for your project can be done in 'tex/src/preamble-project.tex', so you don't have to worry about any other LaTeX preamble file. They are either templates (like the ones for PGFPlots and BibLaTeX) or low-level things directly related to Maneage. Until now, this distinction wasn't too clear. Here is a summary of the improvements: - Two new options to './project make': with '--highlight-new' and '--highlight-notes' it is now possible to activate highlighting on the command-line. Until now, there was a LaTeX macro for this at the start of 'paper.tex' (\highlightchanges). But changing that line would change the Git commit hash, making it hard for the readers to trust that this is the same PDF. With these two new run-time options, the printed commit hash will not changed. - paper.tex: the sentences are formatted as one sentence per line (and one line per sentence). This helps in version controlling narrative and following the changes per sentence. A description of this format (and its advantages) is also included in the default text. - The internal Maneage preambles have been modified: - 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have been merged into one preamble file called 'tex/src/preamble-maneage-default-style.tex'. This helps a lot in simply removing it when you use a journal style file for example. - Things like the options to highlight parts of the text are now put in a special 'tex/src/preamble-maneage.tex'. This helps highlight that these are Maneage-specific features that are independent of the style used in the paper. - There is a new 'tex/src/preamble-project.tex' that is the place you can add your project-specific customizations.
2020-11-30Comments to help clarify the roles of input files in paper.texMohammad Akhlaghi-1/+4
These can help a first-time reader of 'paper.tex'.
2020-11-30New tex/src/preamble-maneage.tex for Maneage-only TeX customizationMohammad Akhlaghi-1/+2
Until now, the Maneage-only features of LaTeX where mixed with 'tex/src/preamble-project.tex' (which is reserved for project-specific things). But we want to move the highlighting features (that have started here) into the core Maneage branch, so its best for these Maneage-specific features to be in a Maneage-specific preamble file. With this commit, a hew 'tex/src/preamble-maneage.tex' has been created for this purpose and the highlighting modes have been put in there. In the process, I noticed that 'tex/src/preamble-project.tex' doesn't have a copyright! This has been corrected.
2020-11-30Summarized Roberto's CV, further summarized Raul's and Mohammad'sMohammad Akhlaghi-9/+6
Roberto sent me his summarized CV which is now being included and I also removed the extra statements about non-degree things from Raul and my own biography (like mentioning Gnuastro, and scientific interests). To be short, we are only mentioning degrees and positions. For Raul, I added his M.Sc institute.
2020-11-30Imported improved definition that is made better after discussionMohammad Akhlaghi-5/+5
After Mohammad-reza sent me his commit on an improved definition for longevity, we had an indepth discussion (through a video-conference) to avoid complexities in the terminology, while staying on point and word-count. In this commit/merge, I am including the improved version of the definition of longevity, and the newly added term "functionality" (instead of "usability" that Mohammad-reza was originally complaining to).
2020-11-30Minor edit in paragraph on execution timeMohammad Akhlaghi-6/+6
The paragraph was slightly shortened, while keeping the main points.
2020-11-30Rephrased longetivity definitionMohammadreza Khellat-3/+4
Before this commit, Longetivity was defined on the basis of the term usability. Although the scope and context of the term has been mentioned right after its use, this could have caused confusion with the keyword "usability" in the field of software engineering. With this commit, Longetivity definition has been rephrased in a way that it would not require "usability". Furthermore, since longetivity would logically require the availability of the machines and platforms during the time of re-use, this has been explicitly mentioned in the definition.
2020-11-28Shorter biography for RaulRaul Infante-Sainz-3/+2
Following Boud's great suggestion, I also summarized my CV to be less than 40 words.
2020-11-27Shorter biography for MohammadMohammad Akhlaghi-8/+7
Following Boud's great suggestion, I also summarized my CV to be less than 40 words.
2020-11-27Shorter CVs for boud+davidBoud Roukema-10/+4
This commit provides shorter CVs for me (Boud) + David in order to get closer to the 6500 word limit. Our CVs are the least significant part of the paper.
2020-11-27Merged with Boud's corrected answers (generally very similar)Mohammad Akhlaghi-7/+8
The only issue that still remains is how to address statistical reproducibility, and I am in touch with Boud to do this in the best way possible (it has been highlighted with '#####'s in the answers.