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2020-05-22Re-write of the paper to fit in ~6000 words and IEEE formatMohammad Akhlaghi-31/+74
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-14/+48
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.
2020-05-01Imported recent changes in Maneage, minor conflicts fixedMohammad Akhlaghi-23/+16
A few small conflicts showed up here and there. They are fixed with this merge.
2020-05-01Added interesting references by DavidMohammad Akhlaghi-0/+31
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.
2020-04-23Further edits to summarize the parts corrected by BoudMohammad Akhlaghi-4/+4
[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.
2020-04-234.3.5 Project analysis - downloadsBoud Roukema-1/+1
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.
2020-04-22Implemented Konrad's suggestions, minor edits here and thereMohammad Akhlaghi-1/+4
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.
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-77/+56
Until now, throughout Maneage we were using the old name of "Reproducible Paper Template". But we have finally decided to use Maneage, so to avoid confusion, the name has been corrected in `README-hacking.md' and also in the copyright notices. Note also that in `README-hacking.md', the main Maneage branch is now called `maneage', and the main Git remote has been changed to `https://gitlab.com/maneage/project' (this is a new GitLab Group that I have setup for all Maneage-related projects). In this repository there is only one `maneage' branch to avoid complications with the `master' branch of the projects using Maneage later.
2020-04-18Two papers cited, for research software and data management plansMohammad Akhlaghi-1/+18
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.
2020-04-17Edited the text, normal sized bibliography and TARGETS.conf in figMohammad Akhlaghi-2/+2
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.
2020-04-14Further text shrink, added Competing interest and Author contributionsMohammad Akhlaghi-8/+22
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).
2020-04-13Full existing contents summaried, only discussion to goMohammad Akhlaghi-1/+1
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.
2020-04-10Renamed initial paper to paper-long.tex, to write shorter new versionMohammad Akhlaghi-0/+2588
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'.
2020-03-31First draft of the version control section and figure completeMohammad Akhlaghi-66/+72
The figure was greatly improved, becoming much more clear and descriptive of some of the main advantages of having version control in a complete project like Maneage.
2020-03-30Section on starting new projects, and publishing project addedMohammad Akhlaghi-5/+165
With the main structure of Maneage explained, I have started to explain how a new project is created, along with a schematic diagram that shows two scenarios of how Git can help with project management.
2020-03-28Cleaned up the introduction, definitions for provenance and lineageMohammad Akhlaghi-1/+35
Until now, the introduction had repeated several things and also had a relatively long list of things to add in its end. Also, it was highly focused to scientific papers. With this commit, I effectively re-wrote it, with the starting paragraphs becoming more industry-friendly, while also focusing on the scientific cases. Many of the repetative parts were removed and the listed items in the end were put into the text in a much better context. Also, now that the name of the system involves "lineage" (and a lot of focus is put on it in the start) the terms data provenance and lineage were defined in the definition section. Some other intersting points that I encountered during the research on definitions were added to the discussion and final lists, and the DOI of one reference paper was corrected.
2020-03-23Analysis and configuration file sections completeMohammad Akhlaghi-28/+126
With this commit a description of these two important parts have been added to the project, along with several figures showing various parts of the files that are discussed. I also done some other restructuring of the figures and files to make things fit better into the the description of the paper.
2020-03-08Menke+20 example: properly count number of papers with softwareMohammad Akhlaghi-1/+1
Until now, I was mistakenly multiplying the fraction of papers in that journal. This is corrected with this commit.
2020-03-08Edited description of example subMakefile for analysis-1Mohammad Akhlaghi-5/+14
In order to make the description more clear and readable, the rules in the demonstrated Makefile (and their links to the data lineage plot) were made more clear.
2020-03-02Described the first analysis phase with a demo subMakefileMohammad Akhlaghi-26/+130
Until now, there was no explanation on an actual analysis phase, therefore with this commit an example scenario with a readable Makefile is included. The Data lineage graph was also simplified to both be more readable, and also to correspond to this new explanation and subMakefile. Some random edits/typos were also corrected and some references added for discussion.
2020-02-16Menke+2020 data is now imported and ready for later steps in plain textMohammad Akhlaghi-1/+1
The main problems with this dataset was the names of the journals (which sometimes have single quotes or apostrophes in them that is really annoying for SED)! But ultimately, for the simple study we want to do here, the journal names are irrelevant, so in the end I just ignored the names. Later we can set an identifier for the journals if necessary. But now we have the basic information in a way that is usable in a plot to show in this paper.
2020-02-15Edits in text, added Menke+2020 as a referenceMohammad Akhlaghi-0/+14
The text was slightly improved/edited and I also recently came up to the Menke et al. 2020 (DOI:10.1101/2020.01.15.908111) which also has some good datasets we can use as a demonstration here.
2020-02-07Edited parts of the textMohammad Akhlaghi-18/+24
While reading over the already written parts (and hopefully complete the paper), they were edited/corrected to be more clear.
2020-02-06Minor edits to various partsMohammad Akhlaghi-17/+54
Some edits were made after rereading of some parts.
2020-01-27Analysis phase description started with Final paper and verificationMohammad Akhlaghi-43/+49
With this commit, the general outline of the analysis phase is given, as well as a description of the LaTeX macros and their relation to the paper and thier verification. Also, the data-lineage figure was updated to have references.tex also and some resizing of the folders in file-architecture to be more clear.
2020-01-26General project structure and configuration describedMohammad Akhlaghi-66/+151
In the last few days I have been writing these two sections in the middle of other work. But I am making this commit because it has already become a lot! I am now going onto the description of `./project make'.
2020-01-20New rendering of the file architecture plotMohammad Akhlaghi-193/+108
Until now the file architecture plot at the directories ontop of the top-level files. This made it hard to visually identify the top-level files. They are not placed ontop of the sub-directories and some space is added to highlight the files in the top-level directory and those in the subdirectories. Two other changes were made: - The symbolic links created in the top source directory are also shown. - The coding of this figure was made much more elegant by defining a PGFPlots node class and just changing the things that are direrent between each directory.
2020-01-20Added figure showing project's file structureMohammad Akhlaghi-3/+252
It was a little hard to describe the file structure so instead of using a standard listing as most papers do, I thought of showing the file and directory structure as boxes within each other (modeled on the Gnome disk-utility). Some other polishing was done throughout the paper also.
2020-01-18Raw draft (until now as a separate repository) importedMohammad Akhlaghi-355/+2157
Until now, I was writing the paper without the template. But we will soon be adding a tutorial to the template, and I thought it will be good to have an example demonstration here too. So I just brought the hole project into the template structure, allowing us to add the template analysis later when its ready, and also allowing us to easily reproduce this paper ofcourse (without having to worry about the host's TeXLive installation.
2020-01-18First set of customizations doneMohammad Akhlaghi-83/+0
The unnecessary parts were removed and the project now runs.
2020-01-01Verification of output values and data added within templateMohammad Akhlaghi-1/+1
Until now, the only verification that the template provided was the published PDF. Users had to manually compare the published and generated PDFs (numbers, plots, tables) and see if they obtained the same result. However, this type of manual verification is not good and is prone to frustration and missing important differences. With this commit, a new Makefile has been added in the analysis steps: `verify.mk'. It provides facilities to easily verify the results that go into the paper. For example tables that go into making the paper's plots, or the LaTeX macros that blend into the text. See the updated parts in `README-hacking.md` for a more complete explanation. This completes task #15497.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-8/+8
Now that its 2020, its necessary to include this year in the copyright statements.
2019-09-15BibLaTeX configured to only print initials of given namesMohammad Akhlaghi-0/+1
Until now, we weren't explicitly asking for BibLaTeX to build the citations with only initial of the author's given names. Therefore when one BibTeX entry had a full given name and another had only initials, this would also be reflected in the paper's bibliography. With this commit, the `giveninits=true' option is given to BibLaTeX to always only print the initial character of an author's given name.
2019-09-07Updates in BibLaTeX preambleMohammad Akhlaghi-0/+8
In some cases, users of the template may not need the other template headers, they may only want `preamble-biblatex.tex'. But `xcolor' needs to be loaded before being able to load the various colors we use in the references. So to be self-consistent, it is loaded. Also, the default style was also printing the month of the publication which is not common. So a line was added to clear the `month' field before building the Bibliography.
2019-08-22Paper's title and author information moved to main paper.texMohammad Akhlaghi-12/+0
Until now, the paper's title and author information were set it `tex/src/preamble-header.tex'. But they are actually shown in the final PDF paper and a much better place to keep them is the top-level `paper.tex'. With this commit, the setting of the title and author names has been moved to `paper.tex', just after importing all the preambles. However, the basic package importation and low-level settings are still set in `tex/src/preamble-header.tex', because they are relatively low-level. This task was suggested by Deepak (Indian Institute of Astrophysics).
2019-05-08TeXLive csquotes packages (needed by BibLaTeX) has been addedMohammad Akhlaghi-0/+7
In the warnings output by LaTeX during the building of a project, I noticed that `csquotes' is recommended for some features of BibLaTeX (a warning was printed) so it is added with this commit.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-5/+5
Until now, the software building and analysis steps of the pipeline were intertwined. However, these steps (of how to build a software, and how to use it) are logically completely independent. Therefore with this commit, the pipeline now has a new architecture (particularly in the `reproduce' directory) to emphasize this distinction: The `reproduce' directory now has the two `software' and `analysis' subdirectories and the respective parts of the previous architecture have been broken up between these two based on their function. There is also no more `src' directory. The `config' directory for software and analysis is now mixed with the language-specific directories. Also, some of the software versions were also updated after some checks with their webpages. This new architecture will allow much more focused work on each part of the pipeline (to install the software and to run them for an analysis).
2019-04-14Replaced all occurances of pipeline in textMohammad Akhlaghi-2/+2
All occurances of "pipeline" have been chanaged to "project" or "template" withint the text (comments, READMEs, and comments) of the template. The main template branch is now also named `template'. This was all because `pipeline' is too generic and couldn't be distinguished from the base, and customized project.
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-30/+9
Until now, the files where the people were meant to change didn't have a proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was wrong because the license does not convey copyright ownership. So the name of the file's original author must always be included and when people modify it (and add their own copyright-able modifications). With this commit, the file's original author (and email) are added to the copyright notice and when more than one person modified a file, both names have their individual copyright notice. Based on this, the description for adding a copyright notice in `README-hacking.md' has also been modified.
2019-04-12Dependency BibTeX entries included only when necessaryMohammad Akhlaghi-250/+9
Until now, there was a single `tex/src/references.tex' file that housed the BibTex entries for everything (software and non-software). Since we have started to include the BibTeX entry for more software, it will be hard to manage the large (sometime unused) BibTeX entries of the software in the middle of the non-software related citations in the text of the paper. Therefore, with this commit, a `tex/dependencies' directory has been made which has a separate BibTeX entry file for each software that needs one. After the software is built, this file is copied to the new `.local/version-info/cite' directory. At the end, the configure script will concatenate all the files in this directory into one file which will later be used with `tex/src/references.tex' by BibLaTeX. This greatly simplifies managing of citations. Allowing us to focus on the software-building and paper-writing citations separately/cleanly (and thus be more efficient in both).
2019-04-12Imported recent corrections, no conflictsMohammad Akhlaghi-0/+115
Some recent corrections that were done by Raul are now merged into the pipeline. There weren't any conflicts.
2019-04-12Fixed some Scipy-related packages citationsRaul Infante-Sainz-12/+42
Until now, the Scipy citation was only one paper and not the correct one (it was the online manual). With this commit, Scipy is properly cited using the two papers. Also some modifications in the `tex/src/references.tex' have been done (remove last page number).
2019-04-12Acknowledged Scipy-related packages: Cython, Matplotlib, Numpy and ScipyRaul Infante-Sainz-0/+85
Until now, name and version of all Python packages were indicated in the final paper, but not the main paper of them (if it exists). With this commit, some Python packages (Cython, Matplotlib, Numpy and Scipy) are now properly acknoledged by citating the source paper. `mpi4py' is also cited although this package is not yet included into the pipeline.
2019-04-12Gnuastro's citation included in its build targetMohammad Akhlaghi-1/+1
With this commit, we are applying the new style of citing software within the build rule of Gnuastro.
2019-04-02Copyright notice added to remaining filesMohammad Akhlaghi-0/+21
After doing a systematic search for files without a copyright notice, a few more were found that didn't have a notice. So a notice was added for them. I used this Bash command to find the files: for f in $(find ./ -type f); do \ if [[ $f != *.git* ]]; then \ n=$(grep -i copyright $f | wc -l); \ echo "$n $f"; \ fi; \ done | awk '$1==0'
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-8/+134
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-02-13Imported recent work on building Python within the pipelineMohammad Akhlaghi-0/+94
Raul Infante-Sainz added the building of Python (along with the Numpy and Astropy packages) into the pipeline. That work is now being merged into the main pipeline branch. There was only this small problem that needed to be fixed: the Python tarball's name after unpacking is actually `Python-X.X.X' (with a captial P), not `python-X.X.X'. This has been corrected with this merge.
2019-02-13Astropy installed in the pipelineRaul Infante-Sainz-0/+94
Astropy was added and one very important thing is that we have to use the pypi tarball (https://pypi.org/) (which is bootstrapped) and not the github tarball.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-0/+617
In order to collaborate effectively in the project, even project members that don't necessarily want (or have the capacity) to do the whole analysis must be able to contribute to the project. Until now, the users of the distributed tarball could only modify the text and not the figures (built with PGFPlots) of the paper. With this commit, the management of TeX source files in the pipeline was slightly modified to allow this as cleanly as I could think of now! In short, the hand-written TeX files are now kept in `tex/src' and for the pipeline's generated TeX files (in particular the old `tex/pipeline.tex'), we now have a `tex/pipeline' symbolic-link/directory that points to the `tex' directory under the build directory. When packaging the project, `tex/pipeline' will be a full directory with a copy of all the necessary files. Therefore as far as LaTeX is concerned, having a build-directory is no longer relevant. Many other small changes were made to do this job cleanly which will just make this commit message too long! Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as in the standard GNU Build system).