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2021-06-08Several minor edits, removed exact value of arXiv's size-limitBoud Roukema-29/+30
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.
2021-06-08Minor edits suggested by David and updating of Zenodo DOIMohammad Akhlaghi-2/+3
David made suggested some minor edits that are now implemented (most importantly that he would not like to be associated with an ORCID ID). I also "saved" a new Zenodo DOI for the final submission of this paper to Zenodo, but "after" obtaining the page number information and other minor things.
2021-06-08Improved appendix on archivalMohammad Akhlaghi-17/+57
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.
2021-06-07Clarifications added to ReproZip in the appendixMohammad Akhlaghi-5/+12
After Boud posted a notice about Maneage in an online forum [1], Rémi Rampin and Vicky Rampin (from the ReproZip project) replied with some notes about our review of ReproZip in Appendix B. We are very grateful to both Rémi and Vicky for looking into it and for their comments, their contribution has been gratefully acknowledged with this commit. The relevant comments are listed below and have been addressed in this commit (see the 'diff' of this commit). - [Rémi Rampin] ReproZip can capture the build step if you want it to, it's just another command. So if you want to trace "make" and "pip install" etc before tracing your actual experiment, you will have all that build information. - [Rémi Rampin] Bundle size is easily fixed by not putting terabyte-sized data in the bundle, which is done by editing a simple configuration file. - [Vicky Rampin] Not all the files in the bundle are compiled/binary files [in relation to the old sentence "ReproZip just copies the binary/compiled files used in a project"]. [1] https://framapiaf.org/@boud/106296894758145705
2021-05-26ReproZip, Popper: minor fixesBoud Roukema-4/+4
This commit contains minor fixes in Appendix B. ReproZip: As Vicky Rampin points out [1], ReproZip typically also includes non-binary files, so I removed "just" and improved the wording. Popper: the Popper URL that we gave is obsolete; at Wayback Machine it redirects to getpopper.io [2], so I've updated this; and I've fixed up the wording ('off of' only exists in US English). [1] https://octodon.social/@VickyRampin/106298214313216228 [2] https://web.archive.org/web/20210425223605/http://falsifiable.us/
2021-05-25Fix typo: s/empemera/ephemera/Boud Roukema-1/+1
2021-05-25Brief notes on archiving as Appendix A.DBoud Roukema-0/+33
This commit adds a few extremely brief and incomplete paragraphs on archiving, including URLs, as what is now subsection D of Appendix A.
2021-05-12Implemented changes of first proof by CiSEMohammad Akhlaghi-5/+5
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).
2021-04-17Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-1/+7
Some minor conflicts (all expected from the commit messages in the Maneage branch) occurred but were easily fixed.
2021-04-09Implemented EiC (Lorena Barba) comments, and added final reviewMohammad Akhlaghi-90/+91
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-1/+1
These are minor last minute copyedits for recently added text, e.g. a git hash is not literally a timestamp.
2021-04-09Comments by IAA's AMIGA team implementedMohammad Akhlaghi-6/+10
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.
2021-04-09Comments by Konrad Hinsen implementedMohammad Akhlaghi-25/+44
Konrad had kindly gone through the paper and the appendices with very good feedback that is now being addressed in the paper (thanks a lot Konrad!): - IPOL recently also allows Python code. So the respective parts of the description of IPOL have been updated. To address the dependency issue, I also added a sentence that only certain dependencies (with certain versions) are acceptable. - On Active Papers (AP: which is written by Konrad) corrections were made based on the following parts of his comments: - "The fundamental issue with ActivePapers is its platform dependence on either Java or Python, neither of which is attractive." - "The one point which is overemphasized, in my opinion, is the necessity to download large data files if some analysis script refers to it. That is true in the current implementation (which I consider a research prototype), but not a fundamental feature of the approach. Implementing an on-demand download strategy is not particularly complicated, it just needs to be done, and it wasn't a priority for my own use cases." - "A historical anecdote: you mention that HDF View requires registering for download. This is true today, but wasn't when I started ActivePapers. Otherwise I'd never have built on HDF5. What happened is that the HDF Group, formerly part of NCSA and thus a public research infrastructure, was turned into a semi-commercial entity. They have committed to keeping the core HDF5 library Open Source, but not any of the tooling around it. Many users have moved away from HDF5 as a consequence. The larger lesson is that Richard Stallman was right: if software isn't GPLed, then you never know what will happen to it in the future." - On Guix, some further clarification was added to address Konrad's quote below (with a link to the blog-post mentioned there). In short, I clarified that I mean storing the Guix commit hash with any respective high-level analysis change is the extra step. - "I also looked at the discussion of Nix and Guix, which is what I am mainly using today. It is mostly correct as well, the one exception being the claim that 'it is up to the user to ensure that their created environment is recorded properly for reproducibility in the future'. The environment is *recorded* in all detail, automatically. What requires some effort is extracting a human-readable description of that environment. For Guix, I have described how to do this in a blog post (https://guix.gnu.org/en/blog/2020/reproducible-computations-with-guix/), and in less detail in a recent CiSE paper (https://hal.archives-ouvertes.fr/hal-02877319). There should definitely be a better user interface for this, but it's no more than a user interface issue. What is pretty nice in Guix by now is the user interface for re-creating an environment, using the "guix time-machine" subcommand." - The sentence on Software Heritage being based on Git was reworded to fit this comment of Konrad: "The plural sounds quite optimistic. As far as I know, SWH is the only archive of its kind, and in view of the enormous resources and long-time commitments it requires, I don't expect to see a second one." - When introducing hashes, Konrad suggested the following useful paper that shows how they are used in content-based storage: DOI:10.1109/MCSE.2019.2949441 - On Snakemake, Konrad had the following comment: "[A system call in Python is] No slower than from bash, or even from any C code. Meaning no slower than Make. It's the creation of a new process that takes most of the time." So the point was just shifted to the many quotations necessary for calling external programs and how it is best suited for a Python-based project. In addition some minor typos that I found during the process are also fixed.
2021-01-12Default LaTeX preamble: some packages moved to preamble-project.texMohammad Akhlaghi-69/+39
Until now, important LaTeX packages like 'caption' (for managing figure captions), 'hyperref' (for managing links) and 'xcolor' (for managing colors) were being loaded inside the optional 'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove this file from loading when you use custom journal sytels. However, these packages will often be necessary after loading special journal styles also. With this commit, these packages are now loaded into LaTeX as part of the 'tex/src/preamble-project.tex' file. This file is in charge of LaTeX settings that are custom to the project and independent of its style. Several other small corrections are made with this commit: - I noticed that './project make texclean' crashes if no PDF exists in the working directory! So a '-f' was added to the 'rm' command of the 'texclean' rule. - As part of the LaTeX Hyperref, we can set general metadata or properties for the PDF (that aren't written into the printable PDF, but into the file metadata). They can be viewed in many PDF viewers as PDF properties. Until now, we were only using the '\projecttitle' macro here to write the paper's title. However, thanks to the recently added 'reproduce/analysis/config/metadata.conf', we now have a lot of useful information that can also go here. So the 'metadata-copyright-owner' is now used to define the PDF author, and the project's 'metadata-git-repository' and commit hash are written into the PDF subject. But to import these, it was necessary to define them as LaTeX macros, hence the addition of these macros in 'initialize.mk'. - Some extra packages that aren't necessary to build the default PDF were removed in 'preamble-project.tex'.
2021-01-07Removed all \new highlights after submission of reviewMohammad Akhlaghi-2/+2
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.
2021-01-07Minor copyedits in appendices, e.g. parenthesesBoud Roukema-5/+7
This commit makes some minor fixes following the hardwired non-numerical solution to the cross-referencing issue between the main article and the supplement, such as fixing "lineage like lineage" and missing closing parentheses. From Mohammad: while re-basing the commit over the 'master' branch, I also added Boud'd name at the top of the copyright holders of the appendices.
2021-01-05appendix.bbl is now included in make dist tarballMohammad Akhlaghi-1/+1
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.
2021-01-05Polished main paper and appendices after a full re-readMohammad Akhlaghi-151/+193
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.
2021-01-04Edits on points raised by RaulMohammad Akhlaghi-10/+12
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.
2021-01-04Very minor corrections to the necessity appendixRaul Infante-Sainz-13/+18
With this commit, I have corrected some minor typos of this appendix. They are very minor corrections.
2021-01-04Minor corrections to the existing solutions appendixRaul Infante-Sainz-87/+104
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.
2021-01-03Spell check on main body and appendicesMohammad Akhlaghi-29/+29
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-136/+137
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).
2021-01-03Updated copyrights of project-specific copyrightsMohammad Akhlaghi-6/+6
Having entered 2021, it was necessary to update the years of all the copyright statements.
2021-01-03Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-5/+5
There were only three very small conflicts that have been fixed.
2021-01-03No links to main body in the appendices in --supplement modeMohammad Akhlaghi-9/+50
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.
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-9/+9
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-1/+2
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-3/+143
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'.
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-9/+9
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.
2020-12-30Each appendix moved to a separate .tex fileMohammad Akhlaghi-0/+1059
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).
2020-12-29Copyedit on Appendix ABoud Roukema-34/+34
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.
2020-12-28Minor edits, updated citation to published Menke+20 paperMohammad Akhlaghi-4/+5
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/+6
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.
2020-12-01Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-8/+19
Some minor conflicts that came up during the merge were fixed.
2020-12-01IMPORTANT: organizational improvements in Maneage TeX sourcesMohammad Akhlaghi-159/+173
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.
2020-11-30New tex/src/preamble-maneage.tex for Maneage-only TeX customizationMohammad Akhlaghi-22/+53
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.
2020-11-27Clickable 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.
2020-11-23First draft of all the points addressed by the refereesMohammad Akhlaghi-4/+217
A new directory has been added at the top of the project's source called 'peer-review'. The raw reviews of the paper by the editors and referees has been added there as '1-review.txt'. All the main points raised by the referees have been listed in a numbered list and addressed (mostly) in '1-answers.txt'. The text of the paper now also includes all the implemented answers to the various points.
2020-11-20Highlighting changes can now be toggled at run-timeMohammad Akhlaghi-5/+9
Until now, the core Maneage 'paper.tex' had a '\highlightchanges' macro that defines two LaTeX macros: '\new' and '\tonote'. When '\highlightchanges' was defined, anything that was written within '\new' became dark green (highlighting new things that have been added). Also, anything that was written in '\tonote' was put within a '[]' and became dark red (to show that there is a note here that should be addressed later). When '\highlightchanges' wasn't defined, anything within the '\new' element would be black (like the rest of the text), and the things in '\tonote' would not be shown at all. Commenting the '\newcommand{\highlightchanges}{}' line within 'paper.tex' (to toggle the modes above) would create a different Git hash and has to be committed. But this different commit hash could create a false sense in the reader that other things have also been changed and the only way they could confirm was to actually go and look into the project history (which they will not usually have time to do, and thus won't be able to trust the two modes of the text). Also, the added highlights and the note highlights were bundeled together into one macro, so you couldn't only have one of them. With this commit, the choice of highlighting either one of the two is now done as two new run-time options to the './project' script (which are passed to the Makefiles, and written into the 'project.tex' file which is loaded into 'paper.tex'). In this way, we can generate two PDFs with the same Git commit (project's state): one with the selected highlights and another one without it. This issue actually came up for me while implementing the changes here: we need to submit one PDF to the journal/referees with highlights on the added features. But we also need to submit another PDF to arXiv and Zenodo without any highlights. If the PDFs have different commit hashes, the referees may associate it with other changes in any part of the work. For example https://oadoi.org/10.22541/au.159724632.29528907 that mentions "Another version of the manuscript was published on arXiv: 2006.03018", while the only difference was a few words in the abstract after the journal complained on the abstract word-count of our first submission (where the commit hashes matched with arXiv/Zenodo).
2020-11-15First edits on the newly added appendices in new formMohammad Akhlaghi-12/+11
With the optional appendices added recently to the paper, it was important to go through them and make them more fitting into the paper.
2020-11-04Appendix of long paper added, optionally we can disable itMohammad Akhlaghi-306/+24
Given the referee reports, after discussing with the editors of CiSE, we decided that it is important to include the complete appendix we had before that included a thorough review of existing tools and methods. However, the appendix will not be published in the paper (due to the strict word-count limit). It will only be used in the arXiv/Zenodo versions of the paper. This actually created a technical problem: we want the commit hash of the project source to remain the same when the paper is built with an appendix or without it. To fix this problem the choice of including an appendix has gone into the 'project' script as a run-time option called '--no-appendix'. So by default (when someone just runs './project make'), the PDF will have an appendix, but when we want to submit to the journal, or when the appendix isn't needed for a certain reason, we can use this new option. The appendix also has its own separate bibliography. Some other corrections made in this commit: 1. Some new references were added that had an '_' in their source, they were corrected in 'references.tex'. 2. I noticed that 'preamble-style.tex' is not actually used in this paper, so it has been deleted.
2020-09-24Gnuastro's analysis configuration files removedMohammad Akhlaghi-2/+2
Until now, the core Maneage branch included some configuration files for Gnuastro's programs. This was actually a remnant of the distant past when Maneage didn't actually build its own software and we had to rely on the host's software versions. This file contained the configuration files specific to Gnuastro for this project and also had a feature to avoid checking the host's own configuration files. However, we now build all our software ourselves with fixed configuration files (for the version that is being installed and its version is stored). So those extra configuration files were just extra and caused confusion and problems in some scenarios. With this commit, those extra files are now removed. Also, two small issues are also addressed in parallel with this commit: - When running './project make clean', the 'hardware-parameters.tex' macro file (which is created by './project configure' is not deleted. - The project title is now written into the default output's PDF's properties (through 'hypersetup' in 'tex/src/preamble-header.tex') through the LaTeX macro. All these issues were found and fixed with the help of Samane Raji.
2020-08-20Data lineage and replicated plot in one rowMohammad Akhlaghi-31/+261
Until now, the replicated plot had the width of the full page and the data lineage graph was under it. Together they were covering more than half of the height of the page! But the plot showing the number of papers with tools really doesn't have too much detail, and all the space was being wasted. With this commit, the plot is now much much thinner and the data lineage graph has been fitted to the right of it.