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2020-06-03Updated .gitattributes to include all files to not mergeMohammad Akhlaghi-4/+3
Following a test merge, I noticed that the '.gitattributes' file is not doing anything about the deleted files and also that all the files in 'tex/src/*.txt' should be added (they are too project-specific). So now it only includes the files that aren't deleted. For the files that are deleted, in the Maneage 'README-hacking.md' file, I added an AWK command to easily remove them.
2020-06-03Adding point on small-ness of final product, some summarizationMohammad Akhlaghi-83/+65
I noticed that we hadn't include the publication of the workflow and the advantage that Maneage provides in this regard. So it was added at the end of the proof-of-concept section. However, it was necessary to summarize some other parts to not increase the wordcount.
2020-06-01Edits by DavidDavid Valls-Gabaud-100/+110
These are some corrections that David sent to me by email and I am committing here.
2020-06-01Implemented Antonio's suggestion and thanked himMohammad Akhlaghi-1/+2
Antonio Diaz Diaz (author of the Lzip program/library), has had a very supportive role in what became Maneage in the last 4 years. For example I really started to appreciate the value of simplicity and archivability while reading Lzip's documentation. Fortunately he also read a recent version of the paper that was again very supportive. Some of the minor points he raised had already been fixed, but using 'supplier' instead of 'server' (in the Free Software) criterion was new so I implemented it here with this commit. With this, I am also thanking him for all his wonderful support and encouragement in the last 4 years.
2020-06-01Minor edits to clarify some of the previous correctionsMohammad Akhlaghi-3/+3
Boud's point about a "random reader" not being a good example case was correct. But "user" also gives it a software perspective that is ofcourse not wrong, its can just be confusing. So I thought of changing it to "interested reader". In the part about the C-library dependency of high-level software, from Boud's correction, I found out that it is very hard to convey what I wanted to say (that separating errors due to C-library implementation and measurement errors will be easy, because they should be on much different scales). But I then corrected it to give it a slightly better tone while mentioning the same thing: that with Maneage we can now accurately measure the effect of the C library.
2020-05-31Mostly minor edits of nearly final versionBoud Roukema-17/+18
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
2020-05-30Corrected a few words for more clarityMohammad Akhlaghi-2/+2
An "internally" was added to the part about core GNU tools accounting for the differences between POSIX-compatible systems. One extra word was also removed in the next sentence.
2020-05-30Corrected a few words to make POSIX-fuzzyness paragraph more clearMohammad Akhlaghi-2/+2
Hopefully, it is more to the point with these few word-corrections.
2020-05-30Discussion on issues with POSIX and minor edits to shorten paperMohammad Akhlaghi-39/+47
Konrad raised some very interesting points in particular about the limitations of POSIX as a fuzzy standard that does not guaratee reproducibility. A relatively long paragraph was thus added in the discussion to address this important point. In order to fit it in, the paragraph on "unwanted competition" was removed since the POSIX issue was much more relevant for a curious reader. Throughout the text, some other parts were edited to decrease the length of the paper while making it easier to read.
2020-05-30Minor edits removing redundant sentencesMohammad Akhlaghi-4/+3
Some of the redundant sentences have been removed and some minor edits made.
2020-05-29Minor tidying of about half a dozen wordsBoud Roukema-11/+11
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.
2020-05-29Edits to the text, making it slightly shorter and more clearMohammad Akhlaghi-62/+54
One major point was that following Konrad's suggestion the issue of not being familiar with the Lisp/Scheme framework of GWL is now removed. We actually mention the main problem we have had with Guix, but also highlight that their solution was one of the main inspirations for this work.
2020-05-29TeX installation crash because of different tarball versions fixedRaul Infante-Sainz-2/+58
Until this commit, when the user have previous TeX tarball already present, the project crashed when trying to re-configure, if there was a newer version of TeX. This is because TeX are updated yearly. With this commit, this bug has been fixed. Now, during the installation of TeX, it checks if this problem happens. If this is the case, then it moves the old tarball, download the new one and install it. If not, it will just install the already present tarball or crash because of any other reason. This probem was recurrent, and each time TeX was updated, the previous tarball had to be removed manually. But now, with this commit, it is done automatically. The detection and fix of this bug has been possible with the help of Mohammad Akhlaghi, thanks!
2020-05-29Adding small paragraph for Raul's biographyRaul Infante-Sainz-1/+4
Until this commit, there was only a small description of me. With this commit, I have added a small paragraph with my biography. I know we are very restricted because of the word limit so I tried to be very short!
2020-05-29Minor typos correctedRaul Infante-Sainz-5/+6
With this commit, I have corrected several minor typos.
2020-05-29Minor corrections in abstract and introductionRaul Infante-Sainz-9/+9
With this commit, I did some minor changes in these Sections. Main changes are: define the contraction `OS' from Operating System and use only `OS' later on, and not use contractions like `isn't'
2020-05-29Cut down biography and inclusion of a mention to reproducibilityRoberto Baena-Gallé-5/+5
Before this commit: Roberto's bio was about 120 words. With this commit: it is now less than 100 words. A comment about reproducibility has been added.
2020-05-29Reproducible research based on open-access papersBoud Roukema-3/+2509
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
2020-05-29pdftotext only called if present in system, minor editMohammad Akhlaghi-6/+8
David and Raul had both reported that because 'pdftotext' wasn't available on their system, the project failed (even though the PDF was built!). So with this commit, we first check if the system has 'pdftotext' and call it only if its is available. Some minor edits were made, building upon Boud's previous commit.
2020-05-29Section V - small changesBoud Roukema-25/+26
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.
2020-05-29Sentence with the clerk who can do it, software as uncountable nounBoud Roukema-2/+2
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
2020-05-29Added top-make.mk as a listing for demonstration, minor editsMohammad Akhlaghi-31/+55
To help show the simplicity of 'top-make.mk', it was included as a listing. I also went over some of Boud's corrections and made small edits. In particular: - The '\label' and '\ref' to a section were removed. I done this after inspecting some of their recent papers and noticing that they generally have a simple flow, without such redirections. - In the part about the RDA adoption grant, I moved the "from the researcher perspective" to the end. Because Austin+2017 is mainly focused on data-center management, not the researcher's. They do touch upon researcher solutions that can help data-base managers, but not directly the researchers. In effect with this grant, they acknowledged that our researcher-focused solution confirms with their criteria for data-base management.
2020-05-29Many small changes to Section IV - proof of concept: maneageBoud Roukema-60/+63
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.
2020-05-28Cherry-pick 7bf5fcd to make merging easierBoud Roukema-6/+3
This series of commits aims to edit sections II+III, but first implements the changes from 7bf5fcd, apart from one that conflicts in the abstract: this commit has ``Maneage'' without `(managing+lineage)` in the abstract. From Mohammad: this commit has been rebased after several other parallel branches, so some things may differ from the message.
2020-05-23Some minor edits on Boud's recent correctionsMohammad Akhlaghi-12/+12
Generally they were great, but after looking through them I thought a hand-full of them slightly changed my original idea so I am correcting them here. Boud, if you feel the changes aren't good, let's talk about it and find the best way forward ;-). They are mostly clear from a '--word-diff', just some notes on the ones that have changed the meaning: * On the "a clerk can do it" quotation, since its so short, I think its better to keep its original form, otherwise a reader may thing there were paragraphs instead of the "to" and we have changed their intention. * In the part where we are saying that the workflow can get "separated" from the paper, I mostly meant to highlight that the data-centers and journals (hosts) may diverge in decades, or one of them may go bankrupt, or etc. Hence loosing the connection. The issue of it evolving can in theory be addressed through version control, so I think this is a more fundamental problem. * In the part about free software, in the list, the original point was the free software that are used by the project, not the project itself (after all, the project itself falls under the "Open Science" titles that is very fashionable these days, but my point here is to those people who claim to do "Open Science" with closed software (like Microsoft Excel!).
2020-05-23Section III edits - 5901 wordsBoud Roukema-43/+43
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.
2020-05-23Section II edits + definition of solutionsBoud Roukema-23/+23
This commit implements quite a few minor changes in section II. The aim of most is to clarify the meaning and remove ambiguity. A few changes are that the reader will normally assume that successive sentences in a paragraph are closely related in terms of logical flow. It is superfluous - and considered excessive - to put too many "Therefore"'s and "Hence"'s in (at least) modern astronomy style. These are supposed to be used when there is a strong chain of reasoning. One change is done in the Introduction, because if we're going to use "solution(s)" throughout to mean "reproducible workflow solution(s)", then we have to clearly define this as jargon for this particular paper. It's probably preferable to RWS - reproducible workflow solution - or RWI - reproducible workflow implementation. But we can't just keep saying "solution" because that has many different meanings in a scientific context. Pdf word count = 5880
2020-05-23Cherry-pick 7bf5fcd to make merging easierBoud Roukema-1/+1
This series of commits aims to edit sections II+III, but first implements the changes from 7bf5fcd, apart from one that conflicts in the abstract: this commit has ``Maneage'' without `(managing+lineage)` in the abstract.
2020-05-23Main text: implement most of David's changesBoud Roukema-31/+33
This commit implements most of David's changes from c76727b, but excluding some, such as the proposal to use 'which' in a restrictive clause in the abstract. This is allowed, but the Fowler brothers' rule tends to followed in science writing: https://ell.stackexchange.com/questions/5/is-there-any-difference-between-which-and-that A few points on the abstract: * an immediate solution = singular * The "immediate, fast short-term" benefits sentence sounded like it was redundantly superfluously repetitively repeating doubled-up information. Hopefully this edit is better. * in the %Conclusion, "solutions" is vague, like people who say "technology" when they're only talking about software, so this edit reminds the reader to make the sentence more self-contained and understandable.
2020-05-23Added TeXLive's ulem package to also be builtMohammad Akhlaghi-1/+1
David reported this problem, it happened right after importing IEEEtran, but for some reason, it didn't happen for me.
2020-05-23Corrected name of listings package when installing it with texliveMohammad Akhlaghi-1/+1
When entering the name of the "listings" package, I had forgot to add the final 's', so it wasn't being installed on a clean system! I didn't have a problem until now, because it remained from previous builds.
2020-05-23Biography style reverted to CiSE PDF mode (different from webpage)Mohammad Akhlaghi-18/+8
After a look at the PDFs of the linked papers of the previous commit and a few 2020 papers, we noticed that the biography format of the webpage and PDFs are different! So it is now back in its old way (which is how biographies are presented in the PDF). A few other minor edits were made in the text.
2020-05-23Affiliations CiSE styleBoud Roukema-6/+19
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
2020-05-23Edits, to make the text more readableMohammad Akhlaghi-84/+81
After one day not looking at the first draft of this new version (commit 7b008dfbb9b2), I went through the text and done some general edits to make its presentation and logic smoother.
2020-05-23Typo and style corrections in the text, Roberto's bio addedRoberto Baena-Gallé-37/+41
Before this commit: several typos were present along the text. With this commit several typos have been corrected (types listed below) and my bio has been added. a) double words b) general typos c) comas after adverbs at the beginning of a sentence d) contractions are removed, e.g., don't vs do not e) three sentences in parenthesis have been removed since I think they were out of context or unnecessary f) etc
2020-05-23Corrected name of produced demonstration tableMohammad Akhlaghi-2/+2
In order to correspond to the updated datalineage plot, the name of the plotted columns was changed to 'columns.txt', but I had forgot to update it in the LaTeX source and since the old file still remained I hadn't noticed. This was found by Boud and corrected.
2020-05-22Re-write of the paper to fit in ~6000 words and IEEE formatMohammad Akhlaghi-159/+428
Following the fact that the DSJ editor decided that this paper doesn't fit into their scope, we decided to submit it to IEEE's Computing in Science and Engineering (CiSE). So with this commit the text was re-written to fit into their style and word-count limitations.
2020-05-02First implementation of style in IEEEtran styleMohammad Akhlaghi-552/+830
The paper is no longer using LuaLaTeX, but raw LaTeX (that saves a DVI), it is so much faster! Initially I had used LuaLaTeX to use special fonts to resemble the CODATA Data Science Journal, but all that overhead is no longer necessary. Therefore I also removed the MANY extra LaTeX packages we were importing. The paper builds and is able to construct one of its images (the git-branching figure) with only 7 packages beyond the minimal TeX/LaTeX installation. Also in terms of processing it is so much faster. The text is just temporary now, and mainly just a place holder. With the next commit, I'll fill it with proper text.
2020-05-01Added a .gitattributes file to avoid merging some filesMohammad Akhlaghi-0/+6
As explained in the new `README-hacking.md', this files greatly helps in avoiding un-necessary conflicts.
2020-05-01Imported recent changes in Maneage, minor conflicts fixedMohammad Akhlaghi-651/+733
A few small conflicts showed up here and there. They are fixed with this merge.
2020-05-01Fixed OpenSSL deprecation bug on some OSs, causing problems in libgit2Boud Roukema-1/+16
Until this commit, the configure step would fail with an error when compiling libgit2 on a test system. The origin of this bug, on the OS that was tested, appears to be that in OpenSSL Version 1.1.1a, openssl/ec.h fails to include openssl/openconf.h. The bug is described in more detail at https://savannah.nongnu.org/bugs/index.php?58263 With this commit, this is fixed by manually inserting a necessary components. In particular, `sed` is used to insert a preprocessor instruction into `openssl/openconf.h`, defining `DEPRECATED_1_2_0(f)`, for an arbitrary section of code `f`, to include that code rather than exclude it or warn about it. This commit is valid provided that openssl remains at a version earlier than 1.2.0. Starting at version 1.2.0, deprecation warnings should be run normally. We have thus moved the version of OpenSSL in `versions.conf' to the section for programs that need to be manually checked for version updates with a note to remind the user when reaching that version. Other packages that use OpenSSL may benefit from this commit, not just libgit2.
2020-05-01Abstract: three minor language editsBoud Roukema-4/+4
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.
2020-05-01Merged David's suggestions, further edited to be more clearMohammad Akhlaghi-7/+5
It is also slightly shorter with this commit, without loosing anything substantial.
2020-05-01Minor edits in abstractDavid Valls-Gabaud-7/+7
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.
2020-05-01Minor edits in abstract, link between analysis and narrative addedMohammad Akhlaghi-3/+3
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.
2020-05-01Several minor edits to the title + abstractBoud Roukema-12/+13
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.
2020-05-01Edited abstract for more clarity, still in the 250 word limitMohammad Akhlaghi-28/+15
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.
2020-05-01Abstract re-organized to be more research-orientedBoud Roukema-7/+28
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.
2020-05-01Abstract re-written to better highlight the uniqueness of ManeageMohammad Akhlaghi-9/+9
This abstract is a first step in order to put more focus on the research aspects of Maneage.
2020-05-01Removed Definition and Summary sections and low-level figuresMohammad Akhlaghi-129/+19
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.