| 1ddefba | Boud Roukema | 01 May 2020, 13:07:38 UTC | 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 |
| a6f5fcd | Boud Roukema | 01 May 2020, 13:01:00 UTC | 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 |
| 8f0ce4a | Mohammad Akhlaghi | 01 May 2020, 11:52:22 UTC | Merged David's suggestions, further edited to be more clear It is also slightly shorter with this commit, without loosing anything substantial. | 01 May 2020, 11:52:22 UTC |
| 4381686 | David Valls-Gabaud | 01 May 2020, 11:37:45 UTC | Minor edits in abstract No need to invent a new word (archive-able) when an existing one (archivable) does the job. One issue that we have not included and which perhaps we could discuss in the paper (space permitting), is that this tool could bypass the use of blockchains in this context. | 01 May 2020, 11:37:45 UTC |
| bff9cb5 | Mohammad Akhlaghi | 01 May 2020, 11:24:08 UTC | Minor edits in abstract, link between analysis and narrative added As discussed by Boud in the previous commit, this is an important feature that was lost in the new abstract. So I added it as a criteria. | 01 May 2020, 11:24:08 UTC |
| 1c20614 | Boud Roukema | 01 May 2020, 03:25:55 UTC | 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 |
| 2e525d9 | Mohammad Akhlaghi | 01 May 2020, 02:29:19 UTC | Edited abstract for more clarity, still in the 250 word limit Boud's suggestions in the previous commit were great and really helped in improving the tone of the abstract (and thus the whole paper shortly!), better putting it in the big picture. I had forgot to give the exact word limit (which was 250), so Boud had set it to a very conservative value of 190, I added around 22 words to better highlight the points we want to make, while still being below the limit. | 01 May 2020, 02:39:38 UTC |
| 8f14213 | Boud Roukema | 01 May 2020, 01:20:50 UTC | Abstract re-organized to be more research-oriented To make this a research article, we either have to present it as a theoretical advance, or as an empirical advance. An empirical research result would be something like doing a survey of users and getting statistics of their success/failure in using the system, and of whether their experience is consistent with the claimed properties and principles of Maneage (e.g. success/failure in creating paper.pdf as expected? was the user's system POSIX? did the user do the install with non-root privileges? was this a with-network or without-network ./project configure ?) This is doable, but would require a bit of extra work that we are not necessarily motivated to do or have the time to do right now. I think it's possible to present Maneage as a theoretical advance, but it has to be worded properly. Maneage is a tool, but it's a tool that satisfies what we can reasonably present as a unique theoretical proposal. Here's my proposed rewrite. I've aimed at minimum word length. I've also included (commented out) keywords for a structured research abstract - these are just for us, as a guideline to improve the abstract. I think "criteria" is safer than "standards". Whether a principle is good or bad tends to lead to debate. Whether a criterion is satisfied or not is a more objective question, independent of whether you agree with the criterion or not. In the rewrite below, we propose a theoretical standard and show that the new standard can be satisfied. Maneage is *used as a tool* to prove that the standard is not too difficult to achieve. Maneage is no longer the subject of the paper. (That won't change the main body of the paper too much, apart from compression, but the way it's presented will have to change, under this proposal.) The title would need to match this. E.g. TITLE.1: Evidence that a higher standard of reproducibility criteria is attainable TITLE.2: Evidence that a rigorous standard of reproducibility criteria is attainable TITLE.3: Towards a more rigorous standard of reproducibility criteria I would probably go for TITLE.3. | 01 May 2020, 02:25:08 UTC |
| 842fd2f | Mohammad Akhlaghi | 01 May 2020, 01:10:03 UTC | Abstract re-written to better highlight the uniqueness of Maneage This abstract is a first step in order to put more focus on the research aspects of Maneage. | 01 May 2020, 01:10:03 UTC |
| ce485fc | Mohammad Akhlaghi | 01 May 2020, 00:50:14 UTC | Removed Definition and Summary sections and low-level figures Given the very strict limits of journals, we needed to remove these sections and images. The removed images are: the `figure-file-architecture', `figure-src-topmake' and `figure-src-inputconf'. In total, with `wc' we now have 9019 words. This will be futher reduced when we remove all the technical parts of the Maneage section, in short, we will only describe the generalities, not any specific details. | 01 May 2020, 00:56:35 UTC |
| 638ec52 | Mohammad Akhlaghi | 30 April 2020, 23:39:39 UTC | Added interesting references by David David suggested some interesting references in particular about the problems with Juypyter notebooks that are now added to the long version of the paper. We'll later decide if/how they can be used. | 30 April 2020, 23:39:39 UTC |
| acb13b9 | Mohammad Akhlaghi | 26 April 2020, 23:35:16 UTC | Thanked Fabrizio, Tamara and Nadia for their support They supported my visit and talk on Maneage at the Barcelona Super Computing center. They have also offerred to read the paper and are providing comments. Also, I noticed that in the author list, we had forgot to put an `,' after Boud's name. That is also corrected here. | 26 April 2020, 23:35:16 UTC |
| 8430c9a | Mohammad Akhlaghi | 25 April 2020, 03:58:45 UTC | Demonstration cloning URL set to https://git.maneage.org/project.git Until now, we were using GitLab as the main Git repository of Maneage. But today I finally setup our own Git repository under `git.maneage.org' and enabled a CGit web interface for a simple and fast viewing of the commits and changes. Since this URL is under our own control, we can always ensure that it will point to somewhere meaningful, on any server so in the long-run its much better than publishing the paper an explicit reliance of `gitlab.com'. | 25 April 2020, 03:58:45 UTC |
| b336c13 | Boud Roukema | 24 April 2020, 16:31:31 UTC | Typo | 24 April 2020, 16:59:45 UTC |
| 8bdf5f8 | Mohammad Akhlaghi | 23 April 2020, 22:05:09 UTC | Minor edits on Boud's great corrections Reading over Boud's edits, I noticed a few other parts that I could summarize more and corrected one or two other parts to fit the original purpose of the sentence better. | 23 April 2020, 22:05:09 UTC |
| 6e2ea98 | Boud Roukema | 23 April 2020, 15:36:12 UTC | 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 |
| 1de931d | Boud Roukema | 23 April 2020, 15:12:56 UTC | Discussion/caveats section. Reduction of about 50 words. There were a couple of expressions that look a bit like some sort of software/research analysis jargon, such as `Research Objects`, `Software Heritage`, `Machine actionable`. Unless these are defined, capitalising them makes the reader assume that there is some well-known formal meaning and that s/he has to search for that him/herself. As lower case expressions, the reader can guess some reasonable meanings of these. The word "embargo" was introduced for proposal 2) to handle the third caveat. | 23 April 2020, 15:12:56 UTC |
| 3c5ae2c | Mohammad Akhlaghi | 23 April 2020, 02:44:13 UTC | Further edits to summarize the parts corrected by Boud [Compared to first submission to DSJ last week with 11436 words in raw PDF, we have decreased the paper by ~1000 words to 10493 :-)] As with the previous commits, the moment Boud changed the structure of sentences, I was able to find the redundancies and remove them! This is a fascinating feature of collaboration I had never felt before: it is so hard to find redundancies in my own raw text, but even a minor correction by someone else suddeny breaks my mental memories/barrier on the sentence, allowing me to be more critical to it! Anyway, besides such corrections, I fixed a few other things: 1) In the DSJ's recently published papers, ther is no `~' between "Figure" and its number. 2) I noticed that in `tex/src/figure-src-inputconf.tex' I was actually using manually input strings for the filename, checksum and size! This was contrary to the whole philosophy of Maneage(!), I must have rushed and forgot! So LaTeX variables are now defined and used. | 23 April 2020, 02:54:26 UTC |
| e27634f | Boud Roukema | 23 April 2020, 00:55:51 UTC | 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 |
| 52e9ae4 | Boud Roukema | 23 April 2020, 00:36:43 UTC | 4.5 Project analysis - multi-user Increase by 5 words. We don't need to give a big warning here, but "Permissions management" is meant to be a brief way of saying that whether or not different users can really read/write/execute in subdirectories will firstly depend on whether the user who cloned Maneage has handled these permissions correctly and whether s/he is able to allow others to edit in his/her subdirectories. Comment: Users would have to check who else is logged in at the time, who else is running jobs, and so on. On a supercomputer this might make sense, to avoid unnecessary recompiles. Anyway, this edit summary is not the place to discuss this... | 23 April 2020, 00:36:43 UTC |
| e1adce4 | Boud Roukema | 23 April 2020, 00:25:43 UTC | 4.4 Project analysis - git branches Reduction by 15 words. "Branch" is fine as a verb, and "off" is fine as a preposition; there's no need for a second preposition. "We branched off the main forest path onto a smaller path". | 23 April 2020, 00:25:43 UTC |
| 59715db | Boud Roukema | 22 April 2020, 23:50:56 UTC | 4.3.6 Project analysis - configure files Length reduction by about 15 words. A semantically significant change is from `leading to more robust scientific results` to `evolves in the case of exploratory research papers, and better self-consistency in hypothesis testing papers`. I said this in a previous commit, but it can't hurt repeating: In the covidian epoch (though not only), it is especially important to distinguish bayesian type exploratory research (typical in astronomy or searching for a good COVID-19 treatment or vaccine) from hypothesis testing (clinical testing in double-blind random access trials with clinical trials methods published on a public registry prior to the trials taking place). In the latter case, you want your results to be analysed consistently with the plan published before the trials even begin, and ideally you want them to be published (or at least posted on the trial registry website) even if your results are insignificant, to avoid a publication bias in favour of significant results. Test homeopathy against placebos in 1000 independent experiments, analyse them all the same way, and 2-3 experiments will be significant at the 3 sigma level... | 22 April 2020, 23:50:56 UTC |
| 708ec3b | Boud Roukema | 22 April 2020, 22:46:20 UTC | 4.3.5 Project analysis - downloads Reduction by about 7 words. I added "internet security" as an extra reason for having all the downloads in a single file. Modularity and minimal complexity in themselves generally contribute to internet security, but in this case, it's obvious that having all the communication with the outside world managed through a single file makes internet security management much simpler. I replaced the "fake URL" by the real one, because at least in the present format, the URL fits in nicely. So both `paper.tex` and `tex/src/figure-src-inputconf.tex` are modified in this commit. | 22 April 2020, 22:46:20 UTC |
| 7bdbef3 | Boud Roukema | 22 April 2020, 22:29:26 UTC | 4.3.4 Project analysis - the analysis itself Reduction by about 20 words - minor rewording. | 22 April 2020, 22:29:26 UTC |
| 2f16793 | Mohammad Akhlaghi | 22 April 2020, 20:23:01 UTC | Acknowledged the help of Idafen in Maneage Idafen has helped in testing Maneage a lot during the last year and has provided very useful feedback and suggestions. | 22 April 2020, 20:23:01 UTC |
| f990bba | Mohammad Akhlaghi | 22 April 2020, 18:49:31 UTC | Applied futher comments by Konrad Regarding Docker Konrad pointed out that "Linux has an excellent track record for stability. It's more likely that the Docker itself becomes incompatible with older containers. Docker isn't developed for reproducibility after all". So I tried to modify that paragraph to include this important point too. In the process, I also shrank it a little more (without loosing anything substantial), so it doesn't add to the paper's length. | 22 April 2020, 18:49:31 UTC |
| 76a2148 | Mohammad Akhlaghi | 22 April 2020, 18:08:35 UTC | Minor edits to summarize section on project.tex and verify.tex After going through Boud's corrections, I thought it can be further summarized without loosing any major point. | 22 April 2020, 18:18:10 UTC |
| c9d6492 | Boud Roukema | 22 April 2020, 17:09:49 UTC | 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 |
| 085141f | Boud Roukema | 22 April 2020, 16:58:43 UTC | 4.3.2 Project analysis - values within text Reduction of about 15 words. The phrase "which does not need it" is removed. On its own, this is a claim, not an explanation. If the reader is wondering why `paper.tex` is not a produced file, then stating that the file is not needed will not help very much. Looking at the diagram will show that `paper.tex` is the overall article template; and the diagram strongly suggests that values from initialize.tex, ..., are passed into verify.tex, and from there into project.tex, which goes into paper.tex. The phrase "files, possibly in another subMakefile" should really be something like "files, possibly created by another subMakefile". But this would add more words, and given that the user has full control to modify and adapt the overall scheme (including making a mess of it), we can safely drop the info that the scheme can be made more complicated. :) | 22 April 2020, 16:58:43 UTC |
| 282be64 | Boud Roukema | 22 April 2020, 16:14:10 UTC | 4.3.1 Project analysis - paper.pdf Only 3 words are reduced in this commit, but I think the improvements are worth it. "Note that" and "It is worth mentioning" are phrases still quite often used by academics (even in astronomy) that can be politely described as "pontification" or informally as "empty blabla"; these add no meaning except "I am teaching you something and I expect you to pay attention to what I am saying". :) There are also less polite descriptions. | 22 April 2020, 16:14:10 UTC |
| 8d88566 | Boud Roukema | 22 April 2020, 16:08:31 UTC | 4.3 Project analysis intro Minor rewording of 4.3 Project analysis - introduction. Reduction of about 40 words. 4.2 `parallel` quote: s/http:/https:/ | 22 April 2020, 16:08:31 UTC |
| f0622d8 | Mohammad Akhlaghi | 22 April 2020, 03:49:16 UTC | Implemented Konrad's suggestions, minor edits here and there Today Konrad made the following suggestions after reading through the paper (created from Commit 1ac5c12). Thanks a lot Konrad ;-). I tried to address them all in this commit. Afterwards, while looking over the corrected parts, some minor edits came up to me to remove redundant parts and add extra points where it helps. In particular to be able to print the International Phonetic Alphabet (IPA), I had to include the LaTeX `TIPA' package, but it was interesting to see that it was already available in the project as a dependency of another package we loaded. | 22 April 2020, 03:58:12 UTC |
| 1f8fca2 | Mohammad Akhlaghi | 20 April 2020, 19:29:19 UTC | Configuration: current directory printed properly in stdout Until now, the message that we printed just before starting to build software didn't actually print the current directory, but only `pwd'. With this commit, this is fixed (it uses the `currentdir' variable that is already found before). | 20 April 2020, 19:29:19 UTC |
| 69e7422 | Mohammad Akhlaghi | 20 April 2020, 17:51:26 UTC | Added link to citation from GNU Parallel, slightly summarized it Boud previously pointed out that that he couldn't find a reference to the citation, so I added it as a link over "its FAQ" (since its described in its `doc/citation-notice-faq.txt' file). I also removed the first part of the quote which was not really necessary, the heart of the quote is the latter part that still remains. | 20 April 2020, 17:51:26 UTC |
| 0321773 | Mohammad Akhlaghi | 20 April 2020, 05:01:30 UTC | Minor edits on Boud's corrections to merge I tried to make it slightly shorter, but I felt that it is important to keep the quote from GNU Parallel and in particular the financial aid it asks for. It will help readers feel the gravity of the sitution for this software author. The precise citation of the quote was given in the long version. | 20 April 2020, 05:03:56 UTC |
| 00500f6 | Boud Roukema | 20 April 2020, 01:18:17 UTC | 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, 05:03:14 UTC |
| c710370 | Boud Roukema | 20 April 2020, 00:59:34 UTC | Minor copyedits - 4.2.1 source verification Minor rewording; a reduction of about 12 words. | 20 April 2020, 05:03:14 UTC |
| 6fed651 | Boud Roukema | 20 April 2020, 00:50:36 UTC | Minor copyedits - 4.2 intro configuration Minor edits - reduces about 17 words. | 20 April 2020, 05:03:14 UTC |
| 30cfbab | Boud Roukema | 20 April 2020, 00:15:25 UTC | Minor copyedits - 4.1 Maneage orchestration This commit reduces about 25 words from the 4.1 Maneage orchestration, aka `make`, section. | 20 April 2020, 05:03:14 UTC |
| e7bf184 | Boud Roukema | 19 April 2020, 23:59:20 UTC | Minor edits to 4 Maneage intro This drops the word count in the introductory part of the Maneage section by about 15 words. | 20 April 2020, 05:03:14 UTC |
| ae4142f | Mohammad Akhlaghi | 20 April 2020, 04:12:16 UTC | Clarfication on free software complementing reproducibility Thanks to Boud's corrections, I see that the sentence can be confusing and not convey the point I wanted to make properly, so I am clarifying it here. The main point is that this principle complements the definition of reproducibility, not the other principls. | 20 April 2020, 04:14:18 UTC |
| 1d72bf8 | Boud Roukema | 19 April 2020, 23:05:22 UTC | minor language edits These tiny language edits add 1 word in length. | 20 April 2020, 04:14:18 UTC |
| c6372f4 | Mohammad Akhlaghi | 20 April 2020, 04:02:24 UTC | Boud moved to third author, Lyon affiliation for Mohammad, minor edits Boud has contributed a lot to Maneage over the last few years and with the last few commits he also contributed significantly to this paper, so I am moving him to third author. Thanks to Boud, I also remembered that even though I done the most important parts of Maneage in Lyon, I hadn't added it as an affiliation for myself, so I added it. Maneage became a separate project in Lyon. Finally, I tried to decrease the length of the acknowledgments by adding some abbreviations that were shared between various parts. | 20 April 2020, 04:02:24 UTC |
| 564b91a | Boud Roukema | 20 April 2020, 00:35:10 UTC | 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, 02:19:34 UTC |
| ce1a5ee | Mohammad Akhlaghi | 20 April 2020, 02:14:21 UTC | Minor edits in the text While looking over the PDF, a few small edits were made to be more clear. | 20 April 2020, 02:14:21 UTC |
| 3a56aac | Mohammad Akhlaghi | 19 April 2020, 19:54:10 UTC | Imported the recent parallel works on the principles section The conflict was only on the list of existing tools and that was easily corrected. | 19 April 2020, 19:54:10 UTC |
| bf6e876 | Mohammad Akhlaghi | 19 April 2020, 19:48:20 UTC | Further summarized the principles section Following Boud's great corrections, I was able to futher summarize this section, decreasing roughly 150 more words from this section. | 19 April 2020, 19:48:20 UTC |
| 6e667d9 | Mohammad Akhlaghi | 19 April 2020, 16:13:45 UTC | List of existing tools made cleaner in LaTeX source Until now the list of existing tools was written in one line which made it hard to read and follow, especially since we added links. It is now expanded into a one-line per item which makes to no difference in the final PDF. | 19 April 2020, 16:13:45 UTC |
| 22f380a | Boud Roukema | 19 April 2020, 15:52:41 UTC | Principles - P7 FOSS Reduction by 15 words. | 19 April 2020, 15:52:41 UTC |
| e8eef37 | Boud Roukema | 19 April 2020, 15:40:37 UTC | Principles - P6 Scalability Reduction by 7 words. For a regular GNU/Linux of other unix-like system user, the bit about ISO C compilers even existing for Microsoft systems more or less says "despite there being no point ever trying to do science on a Microsoft system, you *could* hypothetically compile and run any ISO C program on it". Interesting, but not directly of interest to this user, who is unlikely to actually want to do it. A Microsoft user who thinks that s/he can do science on a Microsoft system will typically think "Microsoft is good, so of course I can run anything I want on it". So the message here could more likely be seen as provocative rather than useful, since this user is unaware of the fundamental problems of Microsoft as an authoritarian, manipulative, centralised organisation providing bad software. So either way, the parenthesis about Microsoft can be safely removed given the space constraints. | 19 April 2020, 15:40:37 UTC |
| 1d281bf | Boud Roukema | 19 April 2020, 15:30:14 UTC | Principles - P5 History and temporal provenance Reduction by 5 words. The term "exploratory research" is intended in the specific sense listed at en.Wikipedia: https://en.wikipedia.org/wiki/Exploratory_research to distinguish it from hypothesis testing. The final phases of clinical (medical) research, for example, to test whether a candidate SARS-CoV-2 vaccine is (i) effective and (ii) safe in homo sapiens, cannot accept the exploratory methods that are acceptable in astronomy, or in other exploratory research (which is acceptable in the early stages of medical research). Clinical trial registration is aimed at *preventing* scientists from modifying their methods in a given project: https://en.wikipedia.org/wiki/Clinical_trial_registration | 19 April 2020, 15:30:14 UTC |
| e8f5b6a | Boud Roukema | 19 April 2020, 15:22:59 UTC | Principles - P4 verifiable inputs and outputs One superfluous word was removed. | 19 April 2020, 15:22:59 UTC |
| 4e9e145 | Boud Roukema | 19 April 2020, 15:20:46 UTC | Principles - P3 minimal complexity Minor wording changes - reduction by 10 words. | 19 April 2020, 15:20:46 UTC |
| 13d0a68 | Boud Roukema | 19 April 2020, 15:14:18 UTC | principles - P2 modularity Minor wording improvements; reduction by 10 words. | 19 April 2020, 15:14:18 UTC |
| a133918 | Boud Roukema | 19 April 2020, 15:03:53 UTC | principles: all nouns For consistency, the principles should either all be nouns, or all be adjectives. Most are nouns, so this commit switches the adjectives to nouns. | 19 April 2020, 15:03:53 UTC |
| 6e97fdd | Boud Roukema | 19 April 2020, 14:55:51 UTC | Principles - P1 - Complete Compression by about 40 words. Updating python2 to python3 is often nothing more than modifying print statements, so removing this doesn't weaken the text by much. Re-creation helps avoid thinking of watching movies, going to the beach, reading a novel, when seeing the word "recreation": https://en.wiktionary.org/wiki/recreation#Usage_notes The matplotlib sentence was not so clear: now it's a bit shorter and hopefully clearer. | 19 April 2020, 14:55:51 UTC |
| 49cdb17 | Boud Roukema | 19 April 2020, 14:17:04 UTC | Principles intro Word-length reduction (8 words) of the first part of 3 Principles. Change in meaning: we can argue that *results* are not part of science, but science needs aims as well as methods; hypotheses are needed too, but these overlap between the aims and methods. So I put "primarily". | 19 April 2020, 14:17:04 UTC |
| e682332 | Boud Roukema | 19 April 2020, 13:58:51 UTC | Clickable URLs for the 19 earlier reproducibility solutions In this commit, the URLs for the 19 "earlier solutions" at the beginning of "3 Principles" are recovered from tex/src/paper-long.tex and put behind the package names as clickable words. To reduce the chance that these are interpreted as references, "Project1 (yyy1), Project2 (yyy1)" is changed to "yyy1: Project1, Project2". We cannot add full references because of the 8000-word space constraint. With a minor word improvement, this commit overall reduces the word count very slightly, by 9, according to pdftotext paper.pdf |wc paper.txt before and after the commit. | 19 April 2020, 13:58:51 UTC |
| d4fb323 | Mohammad Akhlaghi | 18 April 2020, 17:49:26 UTC | Added arbitrarily complex to description of scalability Scalability is not just on the size of the project, but also its complexity, so I added an `and/or complex' to the description of the scalability principle. | 18 April 2020, 17:49:26 UTC |
| c7969da | Mohammad Akhlaghi | 18 April 2020, 17:02:53 UTC | Added Scalability as a principle, minor edits/clippings Someone reading the principles section until now would think that IPOL is an almosts perfect solution, and for its usecase it certainly is. However, this is only because of the nature of its work: it only focuses on algorithms, not usage/analysis which cannot be done in raw ISO C. So with this commit, I added a new principle on Scalability and discussed this limitation of IPOL there. To avoid simply lengthening the text, to add this new principle, I had to remove/summarize some parts that seemed redundant. In the process, I also removed some of the existing tools (at the start of the principles section) that had several others in the same time frame, I have already mentioned (through the "and many more") that this list is not complete. Also, the list of people to thank in the acknowledgments is now put in a one-line per name to be more easily maintainable: Boud and Mohammad-reza were added, and given that I have sent the paper to several other people for feedback, I expect the list to get longer. | 18 April 2020, 17:14:09 UTC |
| 063b74c | Boud Roukema | 18 April 2020, 15:16:49 UTC | Minor language edits in paper.tex A few more minor language edits. For parseable vs parseable, see https://en.wiktionary.org/wiki/parsable which recommends `parsable` for formal usage. | 18 April 2020, 16:09:17 UTC |
| 9ac77d0 | Boud Roukema | 18 April 2020, 14:02:26 UTC | Minor language edits in paper.tex These are mostly minor language edits. There is one significant fix: the word `typically' in `a non-free software project typically' cannot be distributed by the project. There is a whole range of licences between strictly free software definition, strictly OSI open-source definition, and fully closed source. For example, software with a no-commercial usage licence (similar to CC-BY-NC) can be publicly redistributed on any server, as long as there is no requirement of payment or no requirement of payment that is "commercial" (according to lawyers' interpretation of when a payment is commercial). | 18 April 2020, 16:07:26 UTC |
| 83fea23 | Mohammad Akhlaghi | 18 April 2020, 02:46:16 UTC | Two papers cited, for research software and data management plans These are important aspects that are highly relevant to Maneage: its philosophy (the former) and usability (the latter). To add them, I tried to summarize some other parts of the paper. | 18 April 2020, 02:46:16 UTC |
| e9b55c9 | Mohammad Akhlaghi | 18 April 2020, 00:13:45 UTC | Imported recent updates in Maneage, no conflicts There weren't any conflicts in this merge. | 18 April 2020, 00:13:45 UTC |
| a323fe1 | Roberto Baena-Gallé | 17 April 2020, 13:56:10 UTC | Corrected several instances of n't to not Three such cases and they are fixed. | 18 April 2020, 00:04:19 UTC |
| c003a2d | Mohammad Akhlaghi | 17 April 2020, 23:51:20 UTC | Edits in the text to make it shorter and fix a few mistakes A few minor issues were found and fixed in the text. I also tried to shorten it a little further. | 17 April 2020, 23:51:20 UTC |
| 3a49e2c | Mohammad Akhlaghi | 17 April 2020, 23:34:20 UTC | Properly adding libiconv to the libraries that libstdc++ links with Of the GCC dynamically linked libraries we need to manually add RPATH to all and for `libstdc++' we also need to tell it to link with `libiconv'. Until now, the conditional to check for libstdc++ was not working and thus libiconv wasn't been added to it. With this commit the conditional has been corrected and is now working. Also, to help in reading the logs, an echo statement was added after every call to PatchELF. | 17 April 2020, 23:34:20 UTC |
| d91813a | Mohammad Akhlaghi | 17 April 2020, 22:55:26 UTC | Replaced name of directory under akhlaghi.org as backup server Until now, when a the raw tarball of some software wasn't usable, I would put it under my own webpage, or `akhlaghi.org/reproduce-software'. That same address was also used as a backup server. However, now the project has a proper name: Maneage. So I changed the directory on my own server to `akhlaghi.org/maneage-software'. With this commit, this new address has replaced the old one. But to avoid crashes in projects that haven't yet merged with the main Maneage branch, the old `reproduce-software' still works (its actually a symbolic link to the new directory now). | 17 April 2020, 22:55:26 UTC |
| 5b72310 | Mohammad Akhlaghi | 17 April 2020, 20:11:31 UTC | Removed confusing comment in configure.sh, and extra variable In the previous commit, we remove the `-static' flag from building PatchELF because it wasn't necessary any more. Howver, the comment for the check still included it and could be confusing. This is corrected with this commit. Also, we don't need the `good_static_libc' variable (that was only defined to pass onto PatchELF). This has also been corrected. | 17 April 2020, 20:14:33 UTC |
| 5950fb9 | Mohammad Akhlaghi | 17 April 2020, 19:29:55 UTC | Patchelf is now built dynamically Until a few commits ago, PatchELF was built statically because it was used to patch `libstdc++' at the end of the GCC building phase, but PatchELF also depends on `libstdc++', so it would crash. However, recently when patching the GCC libraries, we don't directly apply Patchelf to the library, first we copy it to a temporary place, do the patching, then put it in its proper place. So the problem above won't happen any more. With this commit, I am thus removing the static flag from patchelf and letting it built dynamically all the time. The main problem was that some systems don't have a static C++ library, so PatchELF couldn't be built statically. Instead of adding more checks, we just fixed the core foundation of the problem. | 17 April 2020, 19:29:55 UTC |
| 9ed594e | Mohammad Akhlaghi | 17 April 2020, 03:02:28 UTC | Imported recent work in Maneage, minor conflicts fixed A few minor conflicts came up that were easily fixed. | 17 April 2020, 03:02:28 UTC |
| f4d998a | Mohammad Akhlaghi | 17 April 2020, 02:54:00 UTC | Minor typo corrections I forgot to put these in the last commit! They are now implemented. | 17 April 2020, 02:54:00 UTC |
| 1ac5c12 | Mohammad Akhlaghi | 17 April 2020, 01:31:20 UTC | Edited the text, normal sized bibliography and TARGETS.conf in fig I had another look at the text and tried to summarize it a little more while also fixing several typos that I had just discovered! In the process, I noticed that we hadn't actually put a link to Maneage's main Git repository! So we now have the URL as a `git clone' command. Also, I thought that its better to show the `TARGETS.conf' file (which we actually talk about) in the file architecture instead of `LOCAL.conf.in' (which we don't talk about any more!). Finally, to be more similar with DSJ, the bibliography is now in normal font size, not footnotesize. | 17 April 2020, 01:31:20 UTC |
| 8eb0892 | Mohammad Akhlaghi | 17 April 2020, 00:06:20 UTC | IMPORTANT: software config directly under reproduce/software/config Until now the software configuration parameters were defined under the `reproduce/software/config/installation/' directory. This was because the configuration parameters of analysis software (for example Gnuastro's configurations) were placed under there too. But this was terribly confusing, because the run-time options of programs falls under the "analysis" phase of the project. With this commit, the Gnuastro configuration files have been moved under the new `reproduce/analysis/config/gnuastro' directory and the software configuration files are directly under `reproduce/software/config'. A clean build was done with this change and it didn't crash, but it may cause crashes in derived projects, so after merging with Maneage, please re-configure your project to see if anything has been missed. Please let us know if there is a problem. | 17 April 2020, 00:06:20 UTC |
| 4f834ec | Mohammad Akhlaghi | 15 April 2020, 20:45:47 UTC | A single word correction In the introduction I had mistakenly put "metadata" instead of "workflow", its corrected with this commit. | 15 April 2020, 20:45:47 UTC |
| 10fa40e | Mohammad Akhlaghi | 15 April 2020, 17:08:12 UTC | Acknowledged Ryan O'Connor (from RDA), for his comments Ryan O'Connor is from RDA and my principle contact for the grant. He also kindly went over the first draft of the paper and gave useful and encouraging comments. | 15 April 2020, 17:08:12 UTC |
| 6943a8f | Mohammad Akhlaghi | 15 April 2020, 16:43:57 UTC | Merged Raul's correction in the acknowledgments I had also done this in the main branch, but I noticed this commit later! | 15 April 2020, 16:43:57 UTC |
| 356d113 | Mohammad Akhlaghi | 15 April 2020, 16:21:49 UTC | Commented the note to DSJ editors and referees This was only relevant for the submitted version, so I am committing it until the next submission. | 15 April 2020, 16:21:49 UTC |
| 83db81e | Mohammad Akhlaghi | 15 April 2020, 16:13:11 UTC | Minor typo corrections After the submission and reading through the text another time I found some typo corrections and fixed them. Also now that David is an author, I removed him from the people to acknowledge (David brought this up himself, thanks David ;-)). | 15 April 2020, 16:13:11 UTC |
| 46fa90d | Raul Infante-Sainz | 14 April 2020, 22:49:09 UTC | Removed David from Acknowledgments because he is a co-author Since David is a co-author of the paper, I have removed him from the Acknowledgments paragraph. | 14 April 2020, 22:49:09 UTC |
| ff8c4a2 | Mohammad Akhlaghi | 14 April 2020, 22:04:09 UTC | Added note with link to paper's distribution tarball Since the journal doesn't accept supplementary files during initial submission, I have put this link on the PDF for the referee and editors to access if they want. Also the `tex/img' file was added to the distribution tarball. | 14 April 2020, 22:11:10 UTC |
| 0d468bf | Mohammad Akhlaghi | 14 April 2020, 21:27:38 UTC | Corrected package distribution step and not including BibLaTeX packages I was using some special Bash feature before to ignore the distribution directory itself when copying the files, but that had some problems, so I just used a simple for loop over a `find' command to ignore it. Also, for now, we don't need BibLaTeX sources in the project (that is primarily for arXiv), so to help the referee see a more cleaner contents of this supplement file. | 14 April 2020, 21:27:38 UTC |
| d23ebc5 | Mohammad Akhlaghi | 14 April 2020, 20:51:41 UTC | Imported David's corrections into the main paper Thanks David ;-)! I tried to implement as many as I could. For the time being, I just removed teh `~' between "Section" and its number, and removed the italics on software names. Let's see what the journal editors say about it. Otherwise, most of the suggestions were very good and indeed made the text much better to read. | 14 April 2020, 20:51:41 UTC |
| db5701b | David Valls-Gabaud | 14 April 2020, 19:18:48 UTC | Some corrections to help make the text more clear David submitted these comments by email, I (Mohammad) am committing it into the project. | 14 April 2020, 19:18:48 UTC |
| 2cc4bc2 | Mohammad Akhlaghi | 14 April 2020, 17:35:34 UTC | Further text shrink, added Competing interest and Author contributions To make the text easier to read and further comply with the author guideline, the text was shrank a little more and the two final sections were also added on "Competing interest" and "Author contributions". I also found the CODATA logo on Wikipedia in SVG format (vector graphics), so I replaced the previous pixelated PNG format with the PDF (converted from SVG). | 14 April 2020, 17:35:34 UTC |
| f1794e8 | Mohammad Akhlaghi | 14 April 2020, 14:31:21 UTC | Addressed points raised by Raul in previous commit I removed the part emphasizing one journal, but about the comment at the end of the conclusion (to say some negative things): we have already done that in the discussion, mentioning the caveats ;-). But you are right, we should summarize the caveats is well. | 14 April 2020, 14:34:54 UTC |
| 03487ed | Raul Infante-Sainz | 14 April 2020, 11:53:26 UTC | Minor typos fixed up to Section 6: Discussion With this commit, minor typos have been fixed from Section 4 to 6. The majority of them are minor corrections (typos/spelling). I added just a couple of comments/suggestions in red. If you think they are necessary try to fit with the latest modifications. If not, just ignore them. Really nice paper, congratulations to all contributors!! | 14 April 2020, 11:53:26 UTC |
| 9a946b5 | Raul Infante-Sainz | 14 April 2020, 10:00:10 UTC | Minor typos fixed up to Section 3: Principles With this commit, just minor typos have been fixed (I am rushing over the text since we are out of time!). There are also a suggestion in order to remove a couple of phrases to try to be more aseptic when comparing with another project. But there is only an idea, take it or not as you consider. | 14 April 2020, 10:00:10 UTC |
| de23a68 | Mohammad Akhlaghi | 14 April 2020, 05:00:43 UTC | Added first summarized draft of discussion and conclusions A first draft for these was added and will probably become much better in the next few iterations. | 14 April 2020, 05:00:43 UTC |
| 08091a0 | Mohammad Akhlaghi | 14 April 2020, 03:35:53 UTC | Edited/shortened the main body, first draft of summarized discussion I went through the whole paper and tried to decrease its size even futher, also a first draft of the summarized discussion has been added. | 14 April 2020, 03:35:53 UTC |
| 817b196 | Mohammad Akhlaghi | 13 April 2020, 20:51:16 UTC | Installation year removed from TeXLive installation TeXLive recently transitioned from its 2019 version to its 2020 version thanks to Elham Saremi's trial of the this project. The fact that traditionally Maneage installs all TeXLive packages in a per-year directory is very annoying and required an update in the core Maneage system every year. So I suddently recognized that we can fix this by setting a different name for the directory holding the release year. This has been implemented with this commit. I have also done this change in the main Maneage branch for other projects to also benefit from this correction. | 13 April 2020, 20:55:00 UTC |
| e0a57ef | Mohammad Akhlaghi | 13 April 2020, 20:48:59 UTC | Configure (TeXLive): year correction also in high-level packages In the previous commit, I removed the year from the basic installation of TeXLive packages, but I forgot to correct this in the high-level TeXLive packages! This is corrected with this commit. | 13 April 2020, 20:48:59 UTC |
| 7523206 | Mohammad Akhlaghi | 13 April 2020, 20:39:55 UTC | Configure (TeXLive): Year of distribution no longer in directory It is this time of year again: TeXLive has transitioned to its 2020 release and the year is imprinted into the installation directory of TeXLive. Until now, we have had to manually change this year and it caused complications and was very annoying. With this commit, the explicit year has been removed from TeXLive's installation and we now simply put a `maneage' instead of the year. I tried this on another system and it worked nicely. Until the time that we can fully install LaTeX packages from source tarballs, this is the best thing we could do for now. | 13 April 2020, 20:39:55 UTC |
| bdbff0b | Mohammad Akhlaghi | 13 April 2020, 17:04:08 UTC | Implemented Roberto's raised points in the paper's source Thanks Roberto, they are now implemented. | 13 April 2020, 17:04:08 UTC |
| 7ebc882 | Roberto Baena Gallé | 13 April 2020, 16:28:45 UTC | Minor corrections and thoughts I corrected bugs, typos, double words, and punctuations along the whole text. I do some comments which are always highlighted with \hl{this is my comment}, so you can identify them easily in the pdf. If you want to remove, then you can do it easily with Ctrl+R since I think you never used \hl. Finally, I added my name as coauthor but, please, feel free to remove it if you want. Note from Mohammad: since there were two other suggested commits before this that were already merged, I rembased Roberto's commits and fixed a few minor conflicts. | 13 April 2020, 16:37:34 UTC |
| 2aa52db | Mohammad Akhlaghi | 13 April 2020, 16:22:51 UTC | Imported Pedram's corrections, no conflicts There weren't any conflicts in this merge. | 13 April 2020, 16:22:51 UTC |
| 5a00d96 | Raul Infante-Sainz | 13 April 2020, 10:23:04 UTC | Added short line to inform that there are tutorials With this commit, a short line telling that Maneage has tutorials showing the workflow in a practical way has been added. Because of we are near to the limit of words, I have added just a very short line. The sentence does not specify any file name since the tutorial(s) is not included (it will be in a near future). | 13 April 2020, 10:23:04 UTC |
| e965690 | Raul Infante-Sainz | 13 April 2020, 10:02:39 UTC | Adding Julia to acknowledgments for creating the logo With this commit, I have included a small line to recognize Julia Aguilar-Cabello as the designer of the Maneage's logo. | 13 April 2020, 10:02:39 UTC |
| defaeef | Pedram Ashofteh Ardakani | 13 April 2020, 08:27:11 UTC | Fix typos | 13 April 2020, 08:27:11 UTC |
| 16fbab2 | Mohammad Akhlaghi | 13 April 2020, 06:06:53 UTC | Full existing contents summaried, only discussion to go The contents until two commits ago when I started to summarize the paper are now in a new and shorter format: previously the discussion started on page 25, but now it starts on page 17. It is still a little longer than 8000 words, but not as significantly as before. I will add the discussion and also try to summarize it futher before submission. | 13 April 2020, 06:06:53 UTC |
