| HEAD | 54e4eb2 | Updated SoftwareHeritage IDs (SWHIDs) to previous commit Until now, the SWHIDs mentioned in the paper were for the published version of this paper, but updates have come since then, so to be complete in the final arXiv release, it is important that they point to the most recent status before it. With this commit, the relevant SWHIDs of this paper (and Maneage itself) now point to the most recent commit (last commit). | 09 May 2022, 22:25:46 UTC |
| refs/heads/maneage | f51b5e2 | ./project: make clean removes extra tex files in top source directory Until now, the './project make clean' command would only clean (remove) the PDF file from the top source directory. However, if a user would run LaTeX outside of Maneage, many extra latex output such as *.aux, *.log, *.synctex and etc would be produced in the top source directory. These files can interfere with './project make'. With this commit, when './project make clean' is run, any possibly existing LaTeX temporary files will also be deleted from the top source directory. This problem was first reported by Matin Torkian. | 03 May 2022, 19:41:21 UTC |
| refs/heads/master | 54e4eb2 | Updated SoftwareHeritage IDs (SWHIDs) to previous commit Until now, the SWHIDs mentioned in the paper were for the published version of this paper, but updates have come since then, so to be complete in the final arXiv release, it is important that they point to the most recent status before it. With this commit, the relevant SWHIDs of this paper (and Maneage itself) now point to the most recent commit (last commit). | 09 May 2022, 22:25:46 UTC |
| refs/merge-requests/10/head | 6e2ea98 | Conclusion Reduction by about 5 words. Although it's true that the low-level tools - make, bash, gcc - are still being actively developed, only expert users will tend to notice the differences, and in this context, it's probably more useful to point out that these are actively *maintained*. (Comment: I felt that the first sentence in the Conclusion is missing one of the obvious criteria for handling big data - citizen control so that big data could hopefully become less Orwellian than it is right now, with GAFAM having the main big data databases that are used by AI researchers and will tend to affect people's lives more than traditional "scientific" databases. But there's no point adding this here, since the criteria that tend to satisfy the scientific requirements ("principles") and citizens' rights tend to overlap to a fair degree...) | 23 April 2020, 15:36:12 UTC |
| refs/merge-requests/10/merge | 1956806 | Merge branch 'discuss_conclude' into 'master' Discuss conclude See merge request makhlaghi/maneage-paper!10 | 23 April 2020, 15:59:40 UTC |
| refs/merge-requests/11/head | d2d9b9c | Typo | 24 April 2020, 16:31:31 UTC |
| refs/merge-requests/11/merge | a82fdd9 | Merge branch 'typo1' into 'master' Typo See merge request makhlaghi/maneage-paper!11 | 24 April 2020, 17:03:09 UTC |
| refs/merge-requests/12/head | 1c20614 | Several minor edits to the title + abstract Most are minor English tidying, e.g. * spelling: achieving * archivable - https://en.wiktionary.org/wiki/archivable * `i.e.` does not look good in an abstract; * `when` didn't sound quite right; Comment: we no longer state one of the most interesting aspects of Maneage - producing the draft paper that is submittable for peer review in a way that makes it natural for the authors to achieve automatic consistency between the calculations/analysis and the values in the paper. But this is hard to describe in a compact way without disrupting the overall argument of the abstract, so it's a bit of a pity, but people will learn about it anyway from the body of the article (or from trying out the package!) `Peer-review verification` does not directly state producing a pdf. Related to this absence of talking about reproducing the *paper*, not just the calculations, I suggest dropping `, with snapshot \projectversion` from the abstract initially sent to the journal (they can't stop us updating it afterwards), because without the context of explaining that the paper itself is produced from the package, it's not clear what the snapshot means - a snapshot of the abstract? In the `real` paper, it makes sense, because the reader will have access to the rest of the paper. | 01 May 2020, 03:25:55 UTC |
| refs/merge-requests/12/merge | c7346a6 | Merge branch 'abstract_fixes' into 'master' Several minor edits to the title + abstract See merge request makhlaghi/maneage-paper!12 | 01 May 2020, 03:41:26 UTC |
| refs/merge-requests/13/head | a6f5fcd | Abstract: three minor language edits The difference between `that` and `which` is not strictly required, but it helps clarify the difference in meaning, which is important in science and software :). This is best shown by an example: * Maneage provides reproducibility, which is a good thing. The sentence would make sense if we drop `, which is a good thing.` The last part of the sentence is a comment rather than a necessary part of the sentence. * Maneage provides a quality of reproducibility that is missing from other implementations. The sentence would not quite make sense if we drop `that is ...`, since we would not know what sort of quality is provided. The fact that the quality is missing is key to the intended meaning of the sentence. | 01 May 2020, 13:01:00 UTC |
| refs/merge-requests/13/merge | 1ddefba | Merge branch 'abstract_more_fixes' into 'master' Abstract: three minor language edits See merge request makhlaghi/maneage-paper!13 | 01 May 2020, 13:07:38 UTC |
| refs/merge-requests/14/head | b41a646 | Affiliations CiSE style It appears from looking at https://ieeexplore.ieee.org/document/5725236/authors#authors https://ieeexplore.ieee.org/document/7878935/authors#authors that the affiliations section needs to start with a one-phrase definition of the author's main affiliation. In 5725236, the typesetters/proofreaders swapped van der Walt and Colbert, so don't be confused by that. It shows that nobody proofread properly. With this commit, each author's institute (single hierarchical level) is written as the first paragraph of the author's affiliation section. Since 5725236 allows a very-well-known acronym, I'm guessing that IAC can be defined for Mohammad and then re-used for the others. I've added a brief CV for me. If necessary, we could compress my main research together as "observational cosmology", but let's see how we go in the word count. I have not (yet) worked through the main text. There is also one minor language fix - `Because is complete` was incomplete. Pdf word count: 5873 | 23 May 2020, 13:55:03 UTC |
| refs/merge-requests/14/merge | f8b41a5 | Merge branch 'boud_cv' into 'master' Affiliations CiSE style See merge request makhlaghi/maneage-paper!14 | 23 May 2020, 14:00:20 UTC |
| refs/merge-requests/15/head | 660a801 | I. Introduction - minor fixes The changes here should speak for themselves. Use `--word-diff` in either `git diff` or `git log --patch` to see them. | 23 May 2020, 16:03:08 UTC |
| refs/merge-requests/16/head | 112f74b | Section III edits - 5901 words This commit makes several small changes to Section III, some of which are quite significant in terms of meaning. It was difficult to improve the clarity without extending the word length. Now we're at 5901 words. | 23 May 2020, 17:26:50 UTC |
| refs/merge-requests/16/merge | 2628c8c | Merge branch 'boud_sections_II_III' into 'master' Boud sections ii iii See merge request makhlaghi/maneage-paper!16 | 23 May 2020, 17:42:23 UTC |
| refs/merge-requests/17/head | 7f2d535 | Sentence with the clerk who can do it This commit changes two lines. (1) Keeping the exact quote with the clerk while having a sentence that makes sense in plain English cannot be done, it seems to me, without making the sentence a bit longer. Here's one option that seems about the best we can do, even though it still sounds a bit funny, because it's hard to write a future conditional with the present "can". Since it's a quote, it will probably survive the proofreaders. (2) Software is an uncountable noun [1], so we say "software is", like "water is"; "used software" sounds odd; I added "is itself" to emphasise that we're especially talking about the full chain of software for running the project. This commit modifies the "When the ..." sentence and hopefully sounds better. [1] https://en.wiktionary.org/wiki/software#Noun | 24 May 2020, 15:17:47 UTC |
| refs/merge-requests/17/merge | 9c0ec67 | Merge branch 'boud_clerk_can_do_it' into 'master' Sentence with the clerk who can do it See merge request makhlaghi/maneage-paper!17 | 24 May 2020, 15:33:05 UTC |
| refs/merge-requests/18/head | 2627eb2 | Many small changes to Section IV - proof of concept: maneage Possibly the least trivial edit in this commit is that the previous text appeared to state that it's normal to find that a project prepared with `maneage` may be ... unbuildable. Which would defeat our whole claim of reproducibility! Obviously, `maneage` is still in a rapid development stage and might still have significant, not-yet-detected bugs. But the wording has to explain that this would constitute a bug in `Maneage` (in a particular version of it), not an expected regular event. :) This commit aims to fix that and other minor wording issues in IV. Pdf word count 5855. | 23 May 2020, 22:19:17 UTC |
| refs/merge-requests/19/head | 4fb1392 | Section V - small changes This commit provides mostly small changes. There didn't seem much point in repeating the `lessons learned` jargon and claiming that we draw good conclusions - insights - from our experience. Better just state what hypotheses we have generated from the experience rather than give the misleading impression that our hypotheses are well-established facts. In the comments, I put a suggested translation of what the `lessons learned` jargon means. I seem to have first heard this term in the mainstream media a few years after the US 2003 attack on Iraq, when a US military representative stated that the US forces had "learned lessons" after having started a war of aggression against Iraq. Pdf word count: 5921 | 24 May 2020, 17:05:40 UTC |
| refs/merge-requests/19/merge | eecc762 | Merge branch 'boud_section_V' into 'master' Section V - small changes See merge request makhlaghi/maneage-paper!19 | 24 May 2020, 17:19:36 UTC |
| refs/merge-requests/2/head | c917111 | Fix spelling errors, suggest alternative words I tried to get all the words I knew. Some may be correct in different conventions. It definitely needs a second or third review for spell checking. Suggested some additional formatting, including but not limited to using the LaTeX \textsuperscript{} command for stating dates. Also, some unfamiliar rare words that finished with `-able` or `-ability` may need to be changed. Finding better alternatives to better simplify and ease the `readabiliy` ;-) of the paper - I see it's hard not to use them actually. It has got me wondering what better alternatives are available? We'll find out. | 09 April 2020, 18:21:12 UTC |
| refs/merge-requests/2/merge | b15d53e | Merge branch 'branch_pedram' into 'master' Branch pedram See merge request makhlaghi/maneage-paper!2 | 09 April 2020, 18:33:12 UTC |
| refs/merge-requests/20/head | 211665b | Reproducible research based on open-access papers Publishing a paper on reproducible research without making it easy for readers to read the references would defeat the point. Of course we have to make some compromises with some journals' reluctance to shift towards the free world, but to satisfy scientific ethics, we should at least provide clickable URLs to the references, preferably to the ArXiv version if available [1], and also to the DOI, again, preferably to an open-access version of the URL if available. I was not able to fully get this done in the .bst file, so there's an sed/tr hack done to the .bbl file in `reproduce/analysis/make/paper.mk` to tidy up commas and spaces. This commit also reverts some of the hacks in the Akhlaghi IAU Symposium `tex/src/references.tex` entry, to match the improved .bst file, `tex/src/IEEEtran_openaccess.bst`, provided here with a different name to the original, in order to satisfy the LaTeX licence. [1] https://cosmo.torun.pl/blog/arXiv_refs | 24 May 2020, 21:44:38 UTC |
| refs/merge-requests/20/merge | 4ff79fd | Merge branch 'ieee_fix_refs' into 'master' Reproducible research based on open-access papers See merge request makhlaghi/maneage-paper!20 | 24 May 2020, 22:16:17 UTC |
| refs/merge-requests/21/head | 097077d | Minor tidying of about half a dozen words The changes in this commit are best shown with `git diff --word-diff` or `git patch --word-diff`. There are about half a dozen changes of 1-2 words or a comma, the reasons should be obvious. The sentence with "can not just" seems to be correct formally, but "can not only" seems to me better to warn the reader that this is a phrase of the form "can not only do X but can also do Y"; "can not just" sounds a bit like "You cannot just enter the room without knocking" - it doesn't require a second part. | 29 May 2020, 15:25:30 UTC |
| refs/merge-requests/21/merge | a5a4099 | Merge branch 'boud_halfdozen_words' into 'master' Minor tidying of about half a dozen words See merge request makhlaghi/maneage-paper!21 | 29 May 2020, 15:35:43 UTC |
| refs/merge-requests/22/head | 3db3859 | Mostly minor edits of nearly final version Changes with this commit are mostly minor and obvious. Some worth commenting on include: * `technologies develop very fast` - As a general statement, this is too jargony, since technology is much wider than just `software`; `some technologies` makes it clear that we're referring to the specific case of the previous sentence * `in a functional-like paradigm, enabling exact provenance` - While `make` is not an imperative programming language, I don't see how `make` is `like` a functional programming language. Classifying it as a declarative and a dataflow programming language and as a metaprogramming language would seem to go in the right direction [1-3]. I also couldn't see how the language type relates to tracking exact provenance. But since we don't want to lengthen the text, my proposal is to put `and efficient in managing exact provenance` without trying to explain this in terms of a taxonomy of programming languages. [1] https://en.wikipedia.org/wiki/Functional_programming [2] https://en.wikipedia.org/wiki/Comparison_of_multi-paradigm_programming_languages [3] https://en.wikipedia.org/wiki/Dataflow_programming * `A random reader` - In the scientific programming context, `random` has quite specific meanings which we are not using here; a `reader` has not necessarily tried to reproduce the project. So I've proposed `A user` here - with the idea that a `user` is more likely to be someone who has done `./project configure && ./project make`. * `studying this is another research project` - the present tense `is` doesn't sound so good; I've put what seems to be about the shortest natural equivalent. Pdf word count: 5856 | 31 May 2020, 15:52:34 UTC |
| refs/merge-requests/22/merge | 90e1133 | Merge branch 'boud_functional_like_paradigm' into 'master' Mostly minor edits of nearly submitted version See merge request makhlaghi/maneage-paper!22 | 31 May 2020, 16:22:52 UTC |
| refs/merge-requests/23/head | e429b04 | ReproZip, Popper: minor fixes 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/ | 26 May 2021, 00:08:09 UTC |
| refs/merge-requests/23/merge | 606abe7 | Merge branch 'appA_archiving' into 'master' Brief notes on archiving as Appendix A.D See merge request makhlaghi/maneage-paper!23 | 07 June 2021, 19:28:44 UTC |
| refs/merge-requests/24/head | 77ee232 | Several last-minute fixes This commit makes several copyediting changes to the appendices and to the supplement.tex introduction to the appendices. The ArXiv unofficial increased upload limit of 50 Mb is tweeted: 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 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. | 08 June 2021, 17:18:19 UTC |
| refs/merge-requests/24/merge | c4123c9 | Merge branch 'last_minute_fixes' into 'master' Several last-minute fixes See merge request makhlaghi/maneage-paper!24 | 08 June 2021, 17:20:02 UTC |
| refs/merge-requests/25/head | 37ec928 | Fix faulty spell check correction Occured as part of 87b510bc, for original see https://gitlab.com/makhlaghi/maneage-paper/-/blob/94cbed6c63ad4362547b4cbcc579c63937a780a6/paper.tex#L182 | 19 November 2021, 18:40:34 UTC |
| refs/merge-requests/25/merge | 0078cd6 | Merge branch 'fkohrt-master-patch-17031' into 'master' Fix faulty spell check correction See merge request makhlaghi/maneage-paper!25 | 22 November 2021, 22:02:45 UTC |
| refs/merge-requests/3/head | 7a5097b | minor language edits in paper.tex These are all minor. | 18 April 2020, 16:49:22 UTC |
| refs/merge-requests/3/merge | 57d4e60 | Merge branch 'boud' into 'master' Minor language edits in paper.tex See merge request makhlaghi/maneage-paper!3 | 18 April 2020, 16:49:48 UTC |
| refs/merge-requests/4/head | 22f380a | Principles - P7 FOSS Reduction by 15 words. | 19 April 2020, 15:52:41 UTC |
| refs/merge-requests/4/merge | 1e7c59a | Merge branch 'boud' into 'master' Clickable URLs for the 19 earlier reproducibility solutions See merge request makhlaghi/maneage-paper!4 | 19 April 2020, 15:54:06 UTC |
| refs/merge-requests/5/head | 6b00649 | minor language edits These tiny language edits add 1 word in length. | 19 April 2020, 23:05:22 UTC |
| refs/merge-requests/5/merge | cddeb00 | Merge branch 'principles_minor' into 'master' minor language edits See merge request makhlaghi/maneage-paper!5 | 20 April 2020, 04:09:07 UTC |
| refs/merge-requests/6/head | 24cfae2 | Minor copyedits - 4.2.2 software citation This reduces the length by about 70 words. The biggest change is to remove what looks like a citation from `parallel'. I couldn't find the citation in GNU parallel 20161222-1 (Debian/stretch), nor with search engines. I don't think that the quote is really so useful (even assuming it's a valid quote from somewhere): citation practices are a mix between ethics, preparation to convince referees, citing those who are already cited frequently, and the practicality of searching for and verifying references against the information for which they are used. Showing that Maneage makes citation not only easy, but more or less automatic, bypasses some of the compromises between practicality and ethics. | 20 April 2020, 01:18:17 UTC |
| refs/merge-requests/6/merge | 75278c4 | Merge branch 'maneage_section' into 'master' Maneage section See merge request makhlaghi/maneage-paper!6 | 20 April 2020, 04:19:59 UTC |
| refs/merge-requests/7/head | fedf1e3 | boud authorship/affil/acknowl Unfortunately, adding in my name/affiliations/acknowledgments adds about 90 words to the text. We don't really know if these are counted by the editor in the 8000-word limit. I changed `funded' to `funded/supported'. I only get funding from one out of the three sources I acknowledge, but it's important to acknowledge all three. | 20 April 2020, 00:35:10 UTC |
| refs/merge-requests/7/merge | 3b72a96 | Merge branch 'boud_coauthor' into 'master' boud authorship/affil/acknowl See merge request makhlaghi/maneage-paper!7 | 20 April 2020, 02:21:17 UTC |
| refs/merge-requests/8/head | c9d6492 | 4.3.3 Project analysis - verification Reduction by 4 words. Minor rewording; removal of "Note that" and "simply" (the opposite of "complicatedly"). If a checksum is simple for a given user, then s/he already knows that; if s/he doesn't yet know what a checksum is, then stating that it's simple doesn't help very much. :) | 22 April 2020, 17:09:49 UTC |
| refs/merge-requests/8/merge | 0fae58a | Merge branch 'project_analysis_minor' into 'master' WIP: Project analysis mostly minor See merge request makhlaghi/maneage-paper!8 | 22 April 2020, 17:18:32 UTC |
| refs/merge-requests/9/head | e27634f | 4.6 Project analysis - publication About 20 words less. The ArXiv URL is added - this adds no extra length in words, and some readers will not be familiar with ArXiv (although the COVID-19 pandemic has attracted attention to BiorXiv). | 23 April 2020, 00:55:51 UTC |
| refs/merge-requests/9/merge | 2966175 | Merge branch '4_3_analysis_continued' into 'master' 4.3 analysis continued + 4.[56] See merge request makhlaghi/maneage-paper!9 | 23 April 2020, 01:03:41 UTC |
