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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-1/+1
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).
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-4/+1
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-1/+2
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).
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-1/+18
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-0/+116
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).