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2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-87/+87
Having entered 2021, it was necessary to update the copyright years at the top of the source files. We recommend that you do this for all your project-specific source files also.
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/+1061
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-79/+79
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-79/+82
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-6/+93
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
2020-12-14Better warnings when maneage branch not present and PDF not builtMohammad Akhlaghi-12/+31
Until now, there was no warning when the 'maneage' branch didn't exist in the Git history. This can happen when you forget to push the 'maneage' branch to a remote for your project, and you later clone your project from that remote (for example on another computer). We use the 'maneage' branch to report the latest commit hash and date in the final paper (which can greatly help future readers). Since we check the 'maneage' branch on every run of './project make' (in 'initialize.mk') this would result in a printed statement like this: fatal: Not a valid object name maneage Also until now, the description of what to do when TeXLive wasn't installed properly wasn't complete: it didn't mention that it is necessary to delete the TeXLive target files. This could confuse users (they would re-run './project configure -e', but with no effect). With this commit, for the 'maneage' branch issue a complete warning will be printed. Telling the user what to do to get the 'maneage' branch (and thus fix this warning). Also, the LaTeX macros that go in the paper are now red when the 'maneage' branch doesn't exist, telling the user to see the printed warning (thus encouraging the user to get the branch). For the TeXLive issue, the necessary commands to run are now also printed in the warning.
2020-12-09Configuration: not settting C_INCLUDE_PATH on macOSRaul Infante-Sainz-2/+9
Until now, when building the high-level (optional) software, we would give both 'CPPFLAGS' and 'C_INCLUDE_PATH' the same value/directory in 'high-level.mk'. But we recently found that on macOS's C compiler ('clang'), if a directory is included in both 'CPPFLAGS' and 'C_INCLUDE_PATH', then that directory is ignored in 'CPPFLAGS' (which has higher priority). This caused linking problems when the version of a software on the host was different from the Maneage version. With this commit, 'C_INCLUDE_PATH' is not set on macOS any more and this fixed the problem on the reported systems. This bug was fixed with the help of Mohammad Akhlaghi and Mahdieh Navabi.
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-8/+9
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-9/+12
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.
2020-12-02Less is now built as a basic softwareMohammad Akhlaghi-0/+13
Less is rarely used in non-interactive mode and is primarily intended for interactively viewing large files. So its need within Maneage (for batch processing) wasn't often felt until now. However, when running './project shell' (which completely closes-off the outside environment), or building a Maneage'd project within a minimal container that doesn't have less, it becomes hard to use Git (and in particular its 'diff' output which depends on 'less'). With this commit, Less has been added as a dependency of Git in 'basic.mk'. In total its built product is roughly 800KB and builds within a second or two. So it isn't a burden on any project. But it can be very useful when the projects are being developed within the Maneage environment itself.
2020-12-01Installation: m4 no longer depends on TexinfoMohammad Akhlaghi-29/+67
In a recent build on a macOS, we recognized that Texinfo needs the 'libintl.h' headers of Gettext. However, Gettext depends on M4, and until now we had set M4 to depend on Texinfo. Therefore adding Gettext as a dependency of Texinfo would cause a circular dependency. On the macOS, we temporarily disabled M4's Texinfo dependency, and the build went through. I also checked on my GNU/Linux system: temporarily renamed all Texinfo built files from my system and done a clean build of M4 and it succeeded. To be further safe, I built Maneage from this commit (where M4 doesn't depend on Texinfo) in a Docker container, and it went through with no problems. So the current M4 version indeed doesn't need Texinfo. I think adding Texinfo as a dependency of M4 was a historic issue from the early days. In the process, I also cleaned 'basic.mk' a little: - A "# Level N" comment was added on top of each group of software that can be built in parallel (generally). - GNU Nano was moved to the end of the file (to be "Level 6"). - Some comments were edited in some places.
2020-12-01README-hacking.md: recommended to push maneage after mergingMohammad Akhlaghi-4/+11
Until now at the end of the updating process, we hadn't explicity talked about pushing the branches. So people would usually only push their 'master' branch to their remote. While the merged 'master' branch does contain the commits from the core Maneage branch, having a no-updated 'maneage' branch reference on their remote can be confusing. With this commit, at the end of the process to merge with the 'maneage' branch we explicitly recommend to push both the 'master' and 'maneage' branches.
2020-12-01Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-182/+144
Some minor conflicts that came up during the merge were fixed.
2020-12-01Default paper: macros available for date of commits citedMohammad Akhlaghi-5/+12
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-334/+298
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-23/+55
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.
2020-11-28README-hacking.md: updated paper to cite for using ManeageMohammad Akhlaghi-4/+3
Until now, we were asking the users of Maneage to cite the first paper that used its primoridal version (arXiv:1505:01664). But there is now a paper that fully describes the concept (arXiv:2006.03018). With this commit, in the 'citation' section of 'README-hacking.md' we now ask to cite the new paper.
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.
2020-11-27Clickable links in appendicesBoud Roukema-6/+7
This commit makes the numbered links to references such as [13] [14] [15] in the appendices clickable in the pdf. The solution was to call the "\newcites" command from the "multilibs" package *after* loading "hyperref". First do "rm -fv .build/tex/build/*.bbl .build/tex/build/*.aux" and then "./project make" a few times.
2020-11-27Fix paper.bbl flaw; reduce long author lists: save 70 wordsBoud Roukema-10/+21
This commit fixes the error of trying to run bibtex on appendix.tex when the --no-appendix option is selected. A hardwired hack, appropriate only for this specific paper, replaces the more-than-three-author parts of two long author lists by "et al." To test this without having to redownload the menke file, first do "rm -fv .build/tex/build/*.aux .build/tex/build/*.bbl" and then "./project make --no-appendix" a few times. This commit should reduce the word length by about 70 words.
2020-11-27Merged with Boud's corrected answers (generally very similar)Mohammad Akhlaghi-114/+163
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.
2020-11-26All the referee points have been answeredMohammad Akhlaghi-52/+88
There is an answer for all the referee points now. I also did some minor edits in the paper. But we are still over the limit by around 250 words. The only remaining point that is not yet addressed (and has '####' around it) is the discussion on parallelization and its effect on reproducibility.
2020-11-26All questions have now been responded toBoud Roukema-112/+179
This commit is intended to be submittable quality. Point 56 was removed, and the later points renumbered, because it was a point of Reviewer 5 described what we have done - it was not a criticism to respond do. :) The current word count (without abstract and references) is 6091.
2020-11-25Points 33-35 handled in answer to reviewersBoud Roukema-14/+27
This commit only modifies "peer-review/1-answer.txt", giving answers to Reviewer 4; these mostly take into account David's email list of proposed answers. No changes are done to "paper.tex".
2020-11-25Reviewer points 16 to 32Boud Roukema-37/+49
Copyediting of points 16 to 32 (paper.tex + peer-review/1-answer.txt) is done in this commit. TODO list: 2. paper lacking focus 9. tidy up README-hacking.md for appearance on website App B.G. similar to Figure ?? - ref missing 29. website: README-hacking.md and tutorial "on same page"
2020-11-25Reviewer points 1-15; appendix clickable linksBoud Roukema-113/+142
This commit updates "paper.tex" and "peer-review/1-answer.txt" for the first 15 (out of 59!) reviewer points, excluding points 2 (not yet done) and 9 (README-hacking.md needs tidying). A fix to "reproduce/analysis/make/paper.mk" for the links in the appendices is also done in this commit (the same algorithm as for paper.tex is added). The links in the appendices are not (yet) clickable.
2020-11-25Copyedit; no-abstract word count 6084Boud Roukema-31/+37
This commit tidies up minor aspects of the language in the text marked by "\new", e.g. a "wokflow" would be fine for Chinese cooking, but is a little off-topic for Maneage. :) The word count is reduced by about 7 words. I haven't yet got to the serious part: checked that we've responded to the referees' points, and completing the responses which we haven't yet done.
2020-11-24List of answers - minor copyeditBoud Roukema-18/+21
This commit does a minor copyedit of "peer-review/1-answer.txt", mostly just at the top, plus some hashes to highlight an unanswered concern; and removes the @ symbols (and full stops) from email addresses in the peer review email in order to reduce our feeding of email harvesters (spiders that collect email addresses for spammers).
2020-11-23Minor edits and correctionsMohammad Akhlaghi-12/+15
Raul's added point on the answer to the referee was very good, so I edited it a little to be more clear (and removed his name). Also, after looking in a few parts of the text, I fixed a few typos.