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2021-01-03Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-1/+1
There were only three very small conflicts that have been fixed.
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-1/+1
Having entered 2021, it was necessary to update the copyright years at the top of the source files. We recommend that you do this for all your project-specific source files also.
2020-11-04Appendix of long paper added, optionally we can disable itMohammad Akhlaghi-1/+2
Given the referee reports, after discussing with the editors of CiSE, we decided that it is important to include the complete appendix we had before that included a thorough review of existing tools and methods. However, the appendix will not be published in the paper (due to the strict word-count limit). It will only be used in the arXiv/Zenodo versions of the paper. This actually created a technical problem: we want the commit hash of the project source to remain the same when the paper is built with an appendix or without it. To fix this problem the choice of including an appendix has gone into the 'project' script as a run-time option called '--no-appendix'. So by default (when someone just runs './project make'), the PDF will have an appendix, but when we want to submit to the journal, or when the appendix isn't needed for a certain reason, we can use this new option. The appendix also has its own separate bibliography. Some other corrections made in this commit: 1. Some new references were added that had an '_' in their source, they were corrected in 'references.tex'. 2. I noticed that 'preamble-style.tex' is not actually used in this paper, so it has been deleted.
2020-10-02TexLive's xstring package is now necessaryMohammad Akhlaghi-4/+4
After a fresh build of Maneage with a newly downloaded TeXLive, I noticed that it is complaining about not finding 'xstring.sty', apparently some package that depeneded on it is no longer including it itself! It is thus now added to the packages that are built by Maneage's TeXLive.
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.
2020-05-22Re-write of the paper to fit in ~6000 words and IEEE formatMohammad Akhlaghi-1/+3
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-9/+1
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.
2020-04-17Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-0/+27
A few minor conflicts came up that were easily fixed.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-0/+24
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.