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2020-04-19Principles - P1 - CompleteBoud Roukema-19/+19
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.
2020-04-19Principles introBoud Roukema-3/+3
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".
2020-04-19Clickable URLs for the 19 earlier reproducibility solutionsBoud Roukema-1/+1
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.
2020-04-18Added arbitrarily complex to description of scalabilityMohammad Akhlaghi-1/+1
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.
2020-04-18Added Scalability as a principle, minor edits/clippingsMohammad Akhlaghi-20/+38
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.
2020-04-18Minor language edits in paper.texBoud Roukema-7/+7
A few more minor language edits. For parseable vs parseable, see https://en.wiktionary.org/wiki/parsable which recommends `parsable` for formal usage.
2020-04-18Minor language edits in paper.texBoud Roukema-6/+6
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).
2020-04-18Two papers cited, for research software and data management plansMohammad Akhlaghi-40/+53
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.
2020-04-18Imported recent updates in Maneage, no conflictsMohammad Akhlaghi-41/+25
There weren't any conflicts in this merge.
2020-04-18Corrected several instances of n't to notRoberto Baena-Gallé-3/+3
Three such cases and they are fixed.
2020-04-18Edits in the text to make it shorter and fix a few mistakesMohammad Akhlaghi-20/+14
A few minor issues were found and fixed in the text. I also tried to shorten it a little further.
2020-04-18Properly adding libiconv to the libraries that libstdc++ links withMohammad Akhlaghi-1/+4
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.
2020-04-17Replaced name of directory under akhlaghi.org as backup serverMohammad Akhlaghi-17/+17
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).
2020-04-17Removed confusing comment in configure.sh, and extra variableMohammad Akhlaghi-12/+2
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.
2020-04-17Patchelf is now built dynamicallyMohammad Akhlaghi-11/+2
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.
2020-04-17Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-67/+66
A few minor conflicts came up that were easily fixed.
2020-04-17Minor typo correctionsMohammad Akhlaghi-3/+3
I forgot to put these in the last commit! They are now implemented.
2020-04-17Edited the text, normal sized bibliography and TARGETS.conf in figMohammad Akhlaghi-69/+73
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.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-61/+60
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.
2020-04-15A single word correctionMohammad Akhlaghi-1/+1
In the introduction I had mistakenly put "metadata" instead of "workflow", its corrected with this commit.
2020-04-15Acknowledged Ryan O'Connor (from RDA), for his commentsMohammad Akhlaghi-1/+1
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.
2020-04-15Merged Raul's correction in the acknowledgmentsMohammad Akhlaghi-0/+0
I had also done this in the main branch, but I noticed this commit later!
2020-04-15Commented the note to DSJ editors and refereesMohammad Akhlaghi-2/+2
This was only relevant for the submitted version, so I am committing it until the next submission.
2020-04-15Minor typo correctionsMohammad Akhlaghi-12/+11
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 ;-)).
2020-04-14Removed David from Acknowledgments because he is a co-authorRaul Infante-Sainz-1/+1
Since David is a co-author of the paper, I have removed him from the Acknowledgments paragraph.
2020-04-14Added note with link to paper's distribution tarballMohammad Akhlaghi-0/+4
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.
2020-04-14Corrected package distribution step and not including BibLaTeX packagesMohammad Akhlaghi-3/+6
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.
2020-04-14Imported David's corrections into the main paperMohammad Akhlaghi-202/+213
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.
2020-04-14Some corrections to help make the text more clearDavid Valls-Gabaud-261/+261
David submitted these comments by email, I (Mohammad) am committing it into the project.
2020-04-14Further text shrink, added Competing interest and Author contributionsMohammad Akhlaghi-76/+113
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).
2020-04-14Addressed points raised by Raul in previous commitMohammad Akhlaghi-5/+2
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.
2020-04-14Minor typos fixed up to Section 6: DiscussionRaul Infante-Sainz-21/+22
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!!
2020-04-14Minor typos fixed up to Section 3: PrinciplesRaul Infante-Sainz-16/+17
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.
2020-04-14Added first summarized draft of discussion and conclusionsMohammad Akhlaghi-16/+31
A first draft for these was added and will probably become much better in the next few iterations.
2020-04-14Edited/shortened the main body, first draft of summarized discussionMohammad Akhlaghi-267/+188
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.
2020-04-13Installation year removed from TeXLive installationMohammad Akhlaghi-23/+22
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.
2020-04-13Configure (TeXLive): year correction also in high-level packagesMohammad Akhlaghi-1/+1
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.
2020-04-13Configure (TeXLive): Year of distribution no longer in directoryMohammad Akhlaghi-13/+11
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.
2020-04-13Implemented Roberto's raised points in the paper's sourceMohammad Akhlaghi-24/+20
Thanks Roberto, they are now implemented.
2020-04-13Minor corrections and thoughtsRoberto Baena Gallé-99/+101
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.
2020-04-13Imported Pedram's corrections, no conflictsMohammad Akhlaghi-8/+8
There weren't any conflicts in this merge.
2020-04-13Added short line to inform that there are tutorialsRaul Infante-Sainz-0/+1
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).
2020-04-13Adding Julia to acknowledgments for creating the logoRaul Infante-Sainz-0/+1
With this commit, I have included a small line to recognize Julia Aguilar-Cabello as the designer of the Maneage's logo.
2020-04-13Fix typosPedram Ashofteh Ardakani-8/+8
2020-04-13Full existing contents summaried, only discussion to goMohammad Akhlaghi-33/+458
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.
2020-04-12First draft of first three sections of shortened paper are doneMohammad Akhlaghi-0/+418
As described in the previous commit, we had to shorten the paper to roughly 8000 words (which is significant decrease!). With this commit, I am committing the current version of the summarized paper, where the introduction, defintions and principles have now been summarized. I am now summarizing the rest (describing Maneage and the discussion).
2020-04-12Configure (numpy): added --std=c99 to CFLAGS to fix errorMohammad Akhlaghi-0/+1
Elham Saremi recently reported the following errors when building Numpy in numpy/core/src/npysort/radixsort.c.src: "error: 'for' loop initial declarations are only allowed in C99 or C11 mode". After some searching, I found Issue 14147[1] on Numpy's main repository about the same problem. As described there, apparently Numpy needs C99 compiler, but doesn't check for it or set it manually (for some strange reason, leaving it to the packagers to check if they want!!!). Any way, after a check with Elham, we were able to fix it by adding the `--std=c99' to CFLAGS of Numpy's build and with this commit, it is now being implemented in the core Maneage to not cause a problem in any other project. [1] https://github.com/numpy/numpy/issues/14147
2020-04-10Renamed initial paper to paper-long.tex, to write shorter new versionMohammad Akhlaghi-0/+0
We just recently recognied that the final paper should not be longer than 8000 words. The easiest way was just to start a new `paper.tex' and bring in parts from the original/long version. We can use all the hard work that went into writing the long paper later (possibly in a manual for Maneage). So I don't want to suddenly distroy its history at this point. To let Git know about renaming the original `paper.tex' to `tex/src/paper-long.tex', I am making this commit. This commit doesn't have any `paper.tex' and only records the fact that it has been renamed. In the next commit, I'll re-create `paper.tex' which will host the short/final version. But thanks to this commit, if we later make any changes to long version, Git will know that it was originally the main `paper.tex'.
2020-04-10Acknowledged the help of Pedram, Zahra and SurenaMohammad Akhlaghi-0/+1
Thank you very much guys :-).
2020-04-10Fix spelling errors, suggest alternative wordsPedram Ashofteh Ardakani-135/+135
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.